Proteopedia - User contributions [en]

User talk:Anish Sonar

2026-10-08T13:58:37Z

Eric Martz: Welcome!

'''Welcome to ''Proteopedia''!''' We hope you will contribute much and well. You will probably want to watch the narrated [[Proteopedia:Video_Guide|video guide]] and use the [[Help:Contents|help pages]] for later reference. Again, welcome and have fun! . [[User:Eric Martz|Eric Martz]] ([[User talk:Eric Martz|talk]]) 13:58, 8 October 2026 (UTC)

User:Anish Sonar

2026-10-08T13:58:36Z

Eric Martz: Creating user page for new user.

* Position: Student
* Institution: Indian Institute of Science Education and Research Pune
* City: Pune
* State/Province: Maharashtra
* Country: India
* Field of Expertise or Study: Biology

User talk:Lakshit Pareek

2026-10-07T18:00:13Z

Eric Martz: Welcome!

User:Lakshit Pareek

2026-10-07T18:00:13Z

Eric Martz: Creating user page for new user.

* Position: Student
* Institution: Indian Institute of Science Education and Research Pune
* City: Pune
* State/Province: Maharashtra
* Country: India
* Field of Expertise or Study: Biology

User talk:Byung Il Lee

2026-10-06T14:50:06Z

Eric Martz: Welcome!

User:Byung Il Lee

2026-10-06T14:50:06Z

Eric Martz: Creating user page for new user.

* Position: Chief Scientist
* Institution: National Cancer Center
* City: Go-yang si
* State/Province: Gyeonggi-do
* Country: Republic of Korea
* Field of Expertise or Study: Structural biology
* ORCID ID: 0000-0003-1270-8439

User:Eric Martz

2026-10-03T14:07:30Z

Eric Martz:

{| class="wikitable" align="right" width="300"
|[[Image:Eric 1Day Workshop Osaka2009 small.jpg|300px]]
|-
|Teaching at Osaka University, Japan, 2009, in Keiichi Namba's Protonic Nanomachine Group. Photograph courtesy of [[Proteopedia:Scrapbook#Workshops|Akihiro Kawamoto]].
(See T-shirts below.)
|}




Professor Emeritus, University of Massachusetts, Amherst MA USA
<br>
<imagemap>
Image:Youtube.png|left
desc none
default [https://www.youtube.com/channel/UCWNgrSnEfQWaPh3J3mtKhMQ]
</imagemap>
 
{{Template:Martz_email}}
<br clear="left">
Personal website: [https://molviz.org/martz molviz.org/martz]
<br>
[https://scholar.google.com/citations?user=Bb3H0OsAAAAJ&hl=en&oi=ao Publications and Citations]
 
 
 
 
 
 
(([[User:Eric_Martz/Workbench/AccountManagement|quick link for accts]]))
<br>
[https://orcid.org/0000-0003-4679-6967 ORCID ID 0000-0003-4679-6967]

==Proteopedia Pages to Which I've Contributed==
Unless otherwise indicated, these are pages that I created, and for which I provided the initial content.
<br>
Below, -> or <- mean that one page redirects to another page.
===Molecules: Topic Pages===
*I started a stub for [[Antibody]]. Article later written by [[User:David Canner]] and others.
*[[Avian Influenza Neuraminidase, Tamiflu and Relenza]]
**[[Proteopedia:Featured SEL/1]]
*[[Drug and peptide transport in humans]]
** [[Proteopedia:Featured EDU/7]]
** [[Proteopedia:Featured EDU/8]]
*[[Flagella, bacterial]] <- [[Flagellum]], [[Flagellar structure]]
*[[Flagellar filament of bacteria]]
*[[Flagellar hook of bacteria]]
*[[Flaps Morph for HIV Protease]]
*[[Gramicidin Channel in Lipid Bilayer]]
*[[Influenza hemagglutinin]]: I started a stub; article later written by [[User:Savannah Anderson]] and others.
*[[Lac repressor]]
*[[Lipase lid morph]]
*[[Major Histocompatibility Complex Class I]]
*[[Mechanosensitive channels: opening and closing]] included MORPHS
*[[Membrane proteins]]
*[[Metal-Ligand Polyhedra]]
*[[Nitrotyrosine]]
* Nucleosomes: [[User:Eric Martz/Nucleosomes]] (a protected page for lectures), which was copied into [[Nucleosomes]] so others can improve it.
*[[Proton Channels]], which includes an animated morph.
*[[Recoverin, a calcium-activated myristoyl switch]]
*[[Ribosomal A Site Binding Paromomycin: A Morph]]
*[[SARS-CoV-2 protein S priming by furin]]
**[[Proteopedia:Featured_SEL/5]]
*[[SARS-CoV-2 spike protein fusion transformation]]
**[[Proteopedia:Featured_SEL/6]]
*[[SARS-CoV-2 spike protein mutations]]
**[[Proteopedia:Featured_SEL/7]]
*[[Structure of E. coli DnaC helicase loader]] (about a homology model)
*[[SV40 Capsid Simplified]]
*[[Synthetic nanomaterials from standardized protein blocks]]
*[[Thermal motion of peptide]]

===Molecules: PDB Code-Titled Pages===
*[[1hgf]] Influenza hemagglutinin
*[[2ic8]] (green links in overview) Author Ya Ha in 2008 believes the BioUnit is a monomer, though in the 2006 publication, they speculated that it was a trimer. The PDB file deems it a monomer.
*[[2rd0]] Phosphatidylinositol kinase oncogene: I authored scenes similar to many of the figures from the publication.

===Topic Pages: Lists of Other Pages===
*[[About Macromolecular Structure]]
*[[High school teachers' resources]] <- [[K-12 teachers' resources]], [[Secondary school teachers' resources]]
*[[Research Groups|Research Groups and Institutes]]
*[[Structural bioinformatics servers]]
*[[Student Projects]]
*[[Teaching Scenes, Tutorials, and Educators' Pages]] <- [[Molecule of the Month]], [[MotM]], [[Motm]]
* See also [[Topic pages]] -> [[Proteopedia: Topic Pages]]

===Topic Pages - Education===
(Some of these pages are linked redundantly under other headings on this page.)

*[[Proteopedia:News#Adoptions_in_College_and_University_Classes|Adoptions in College and University Classes]]
*[[High school teachers' resources]] <- [[K-12 teachers' resources]], [[Secondary school teachers' resources]]
*[[Molecular Workbench]]
*[[Protein 3D Structure Resources for Educators 2016]]
*Quizzes
**[[User:Eric Martz/Antibody Quiz]]
**[[User:Eric Martz/Antibody Answers]] for open-ended questions provided with the Antibody tutorial at MolviZ.Org
**[[User:Eric Martz/Hemoglobin Quiz]]
**[[User:Eric Martz/MHC Quiz]]
**[[User:Eric Martz/MHC Answers]] for open-ended questions provided with the MHC tutorial at MolviZ.Org
**[[User:Eric Martz/Ramachandran Principle Quiz]]
*[[Student Projects]]
*[[Teaching Scenes, Tutorials, and Educators' Pages]] <- [[Molecule of the Month]], [[MotM]], [[Motm]]
*[[Teaching Strategies Using Proteopedia]]
*[[Technology-Enhanced Science Activities]] for STEMEd 6 Mar 2010
*[[User:Eric Martz/Introduction to Structural Bioinformatics]]

===Topic Pages - Molecular Playground===

* [[Molecular_Playground]]
* [[Molecular Playground/Authoring]]
* [[Molecular Playground/Procedures]]
* [[CBI Molecules]]
::<hr width="10%">
* [[Molecular Playground/HIV Protease Inhibitor]]
**[[Molecular Playground/HIV Protease Inhibitor Enlarged]]
**[[Molecular Playground/HIV Protease Inhibitor/Enlarged]]
* [[Molecular Playground/Relenza]]
* [[Molecular Playground/Tamiflu]]

===Topic Pages - Structural Bioinformatics===
====A-B====
*[[About Macromolecular Structure]]

*[[AlphaFold/Index]], a list of Proteopedia pages about AlphaFold.
*[[AlphaFold]], an introduction and overview.
*[[AlphaFold2 examples from CASP 14]]
*AlphaFold3:
**[[Converting AlphaFold3 CIF to PDB]]
**[[User:Eric Martz/AlphaFold3 case studies]]
*AlphaFold: [[How to predict structures with AlphaFold|How to predict structures from sequences]]
*AlphaFold: [[FirstGlance/How to get average pLDDT from AlphaFold models|How to get average pLDDT]]

*[[Alternate locations]] (initiated by Wayne Decatur)
**[[Alternate locations of backbones]]
*[[Amino Acids]]
*[[Amino acid composition]]
*[[Asymmetric Unit]]
*[[Atomic coordinate file]] <- [[PDB file]], [[PDB file format]]
*[[Backbone representations]]
*[[Biological Unit]] <- [[Quaternary structure]]
*[[Biological Unit: Showing]]
*[[Buried charges detection]]

====C-E====
*[[CASP]]
*[[Cation-pi interactions]] (started by Wayne Decatur)

*Cavities:
**[[Cavity programs]]
**[[Jmol/Cavities pockets and tunnels]]
**[[PACUPP: Pockets And Cavities Using Pseudoatoms in Proteins]]
**[[User:Eric Martz/Cavities tests]]
**[[User:Eric_Martz/Cavity_Notes]]

*[[Chains and Chain IDs]] <- [[Chain]] <- [[Chains]]
*[[Clashes]]
*[[Chimera]]
*[[Conservation, Evolutionary]] <- [[Evolutionary Conservation]]
**[[Introduction to Evolutionary Conservation]]
**[[How to see conserved regions]]
**[[Quick ConSurf Analysis Procedure]]
*[[ConSurf/Index]]
*[[ConSurfDB vs. ConSurf]]
*[[CPK]]
*Crosslinks:
**[[Protein crosslinks]]
**[[FirstGlance/Evaluating Protein Crosslinks]]
*[[Cryo-EM]]
*[[Crystal contacts]]
*[[Cystine]]
*[[Density maps]]
*[[Disulfide bond]]
*[[Domain]]
*[[Drug and peptide transport in humans]]
*[[DRuMS]]
*[[Eric Martz's Favorites]]
*[[Electron cryomicroscopy]]
*[[Electron density maps]]
*[[Electrostatic potential maps]]
** [[Proteopedia:Featured EDU/6]]
*[[Empirical models]]
*[[Epitopes]]
*[[Ester protein crosslinks]]
*Evolutionary conservation: see Conservation
*[[Extremophiles]]

====F-H====
*[[Fadel A. Samatey Group]] also in [[Fadel A. Samatey Group (Japanese)|Japanese]]
*[[Favorites]]
*[[FirstGlance/Index]]
*[[Four levels of protein structure]] -- [[Four levels of protein structure (Spanish)|Los cuatro niveles estructurales de las proteínas]]
*[[Free R]]
*[[Calculating GDT_TS|GDT_TS, calculating]]
*[[Header of PDB file]]
*[[Hetero atoms]]
*[[Highest impact structures]] of all time.
*[[Histidine-tyrosine protein crosslinks]]
*[[History of Macromolecular Visualization]]
*[[Homology modeling]]
*[[Practical Guide to Homology Modeling|Homology Modeling, Practical Guide to]]
*[[Homology modeling servers]]
*[[How to find a protein's best structure]]
*[[How to predict structures with AlphaFold]]
*[[Hydrogen bonds]]
*[[Hydrogen in macromolecular models]]

====I-M====

*[[Improving published models]]
*[[Index pages]]
*[[Influenza]]
*[[Interface analysis servers]]
*[[Interpreting ConSurf Results]]
*[[Intrinsically Disordered Protein]] authored largely by [[User:Tzviya Zeev-Ben-Mordehai]]
*Introductions to
**[[Introduction to Evolutionary Conservation|Evolutionary Conservation]]
**[[Introduction to molecular visualization|molecular visualization]]
**[[User:Eric Martz/Introduction to Structural Bioinformatics|Structural Bioinformatics]]
*[[Isopeptide bond]] <- [[Isopeptide bonds]]
*[[Joining AlphaFold predictions for halves of a molecule]]
*[[Knots in proteins]]
*[[Ligand]]
*[[Lysine-cysteine NOS bonds]] <-- [[NOS]] Disambiguation
*[[Membrane proteins]]
*[[Missing residues and incomplete sidechains]]
*[[Molecular modeling and visualization software]]
*[[Molecular Playground]]
*[[Molecular sculpture]]
*[[Introduction to molecular visualization|Molecular visualization, introduction to]]
*[[Morphs]] of conformational changes of macromolecules <- [[Morph]]
*[[Multiple Protein Sequence Alignment Display with MSAReveal]]

====N-R====
*[[Nitrotyrosine]]
*[[NMR Ensembles of Models]] <- [[NMR]]
*[[Nobel Prizes for 3D Molecular Structure]]
*[[Non-Standard Residues]]
*[[Lysine-cysteine NOS bonds|NOS bonds]]
*[[Proteopedia:Overview|Overview of Proteopedia]]
*[[PDB identification code]] <- [[PDB code]], [[PDB codes]], [[pdb code]], [[pdb codes]]
*[[Peptide]] (page created by Eran Hodis)
*[[Peptide bond]] <- [[Peptide bonds]]
*[[Personal favorites]]
*[[Tutorial:Ramachandran principle and phi psi angles|Phi and psi angles]]
*[[Post-translational modification]] <- [[Post-translational modifications]], [[Posttranslational modification]], [[Posttranslational modifications]]
*[[Protein]] <- [[Proteins]]
*[[Protein crosslinks]]
*[[Protein Data Bank]] <- [[PDB]]
*[[Protein primary, secondary, tertiary and quaternary structure]]
**[[Protein primary, secondary, tertiary and quaternary structure (Spanish)|Los cuatro niveles estructurales de las proteínas]]
*[[Pyrrolysine]]
*[[Quality assessment for molecular models]]
*[[R value]]
*[[Tutorial:Ramachandran principle and phi psi angles|Ramachandran principle and phi psi angles]] (Tutorial) and accompanying [[User:Eric Martz/Ramachandran Principle Quiz|Quiz]]
** [[Proteopedia:Featured EDU/1]]
** See also [[Dihedral/Index]] (initiated by Angel Herráez)
*[[User:Eric Martz/Remarkable Structures|Remarkable Structures]]
*[[RMSD]]
*[[Renumbering PDB files]]
*[[Resolution]]
*[[Retractions and Fraud]]
*[[Ribosomal_A_Site_Binding_Paromomycin:_A_Morph]]

====S-Z====
*[[Salt bridges]]
*[[Sculpting protein conformations]]
*[[Molecular sculpture|Sculpture, molecular]]
*[[Selenocysteine]]
*[[Selenomethionine]]
*[[Unusual sequence numbering|Sequence numbering, unusual]]
*[[Sites | Sites, Functional]]
*[[Standard Residues]] and [[Non-Standard Residues]]
*[[User:Eric_Martz/Introduction to Structural Bioinformatics|Structural Bioinformatics, Introduction to]] aka [http://565.molviz.org 565.molviz.org]
*[[Structural bioinformatics servers]]
*[[Structural genomics]]
*[[Structures_Gallery_Generator]]
*[[Structure superposition tools]]
*[[Suggestions for new articles]]
*[[Structure superposition tools|Superposition tools]]
*[[Teaching Strategies Using Proteopedia]]
*[[Temperature value]] <- [[B value]], [[Disorder]], [[Temperature factor]], [[Temperature]]
*[[Temperature value vs. resolution]]
*[[Temperature color schemes]]
*[[Theoretical models]] <- [[Theory]], [[Theoretical model]]
**[[Proteopedia:Featured_SEL/8]]
*[[Thioester protein cross-links]]
*[[Thioether protein crosslinks]]
*[[Unknown amino acids and nucleic residues]]
*[[Unusual sequence numbering]]
*[[Van der Waals radii]]
*[[FirstGlance/Virus Capsids and Other Large Assemblies|Virus Capsids and Other Large Assemblies]]
** Polio: [[Proteopedia:Featured EDU/4]]
** Eastern Equine Encephalitis virus [[Proteopedia:Featured EDU/5]]
** Bacterial gas vesicles [[Proteopedia:Featured SEL/9]]
*[[Introduction to molecular visualization|Visualization, molecular, introduction to]]
*[[Water in macromolecular models]]
*[[World Index of BioMolecular Visualization Resources]]
*[[X-ray crystallography]] <- [[X-ray diffraction]]

===Art, Molecular===
*[[:Category:PDB_Art]]
*[[Art:Cytochrome_Wallpaper]]
*[[Art:Deconstructing 2GTL]]
*[[Art:Dodecapod]]
*[[Art:Faberge Eggs]]
*[[Art:Five Bakers Dancing]]
*[[History of Macromolecular Visualization]]
*[[Art:Molecular jacks]]
*[[Art:Molecular Sculpture]]
*[[Art:Pentagonal Garden]]
*[[Art:Rainbow_Corn]]
*[[Art:War of the Worlds]]

===Interactive 3D Complements===
* [[User:Fadel_A._Samatey/FlhBc_I]] (April, 2013)
* [[User:Fadel A. Samatey/FlgA I]] (June, 2016)
** [[Proteopedia:Featured JRN/1]]
*[[Malvankar/1]] (March, 2015)
** Animations of pilus model: [http://proteopedia.org/wiki/images/b/b5/Geobacter_pilus_assembling_animation.gif Assembly], [http://proteopedia.org/wiki/images/0/0f/Geobacter_pilus_assembled_rocking.gif Rocking], [http://proteopedia.org/wiki/images/0/0a/Geobacter_pilus_aromatics_rotating.gif Aromatics].
*[[Malvankar/2]] (April, 2019)
** [[Proteopedia:Featured JRN/3]]
*[[Malvankar/3]] (September, 2021)
** [[Proteopedia:Featured JRN/4]]
*[[Ke Xiao/1]] (March, 2016)

*[[Interactive 3D Complements in Proteopedia]] (page started by Jaime Prilusky & David Canner) <- [[I3DC]]
**[[Samatey]], links to I3DC for publications from the Samatey Group.
**[[Malvankar]], links to I3Dc for publications by Nikhil Malvankar ''et al.''
**[[Ke Xiao]], links to I3DC for publications by Ke Xiao ''et al.''

===Topic Pages: People/Biographies===
*[[Richards, Frederic M.]]
*[[Oberholser, Karl]]

===Software===
*[[Molecular modeling and visualization software]]

====Jmol====
*[[Jmol]]
*[[Jmol/Index]] <- [[About Jmol]] [[About JSmol]] [[Help:Jmol]] [[Help:JSmol]]
*[[Jmol/Application]]
*[[Jmol/Visualizing large molecules]]
*[[Jmol/Visualizing membrane position]]: lipid bilayer boundaries.
*[[Jmol/Cavities pockets and tunnels]]
*[[Jmol/Depth from surface]]
*[[Jmol/PDB file editing with Jmol]]
*[[FirstGlance in Jmol]]

====JSmol====
*[[How JSmol Works]] and [[User:Eric Martz/How JSmol works]].
*[[User:Eric Martz/JSmol Notes]] '''<--- TABLE OF EXAMPLE SIZES'''
*[[JSmol/Rotation Speeds]]
* using pspeed to maintain tranlucency, see [[User:Jaime_Prilusky/platformSpeed]]

====FirstGlance====
*[[FirstGlance/Index]] lists related resources within Proteopedia and elsewhere.
*[http://firstglance.jmol.org FirstGlance Entry Page] with links to [http://firstglance.jmol.org/whatis.htm Purpose, Pros & Cons] and [http://tinyurl.com/firstglance1 YouTube: Design Goals and Quick Introduction].
*About [[FirstGlance in Jmol]]
*[[FirstGlance/Evaluating Protein Crosslinks]]
*[[FirstGlance in Jmol Literature Citations]]

====Non-Jmol====
*[[CCP4]]
*[[Chime]]
*[[Java]]
**[[Installing and enabling Java]]
*[[Kinemages, Mage and KiNG]]
*[[Molecular Workbench]]
*[[Protein Explorer]]
*[[PyMOL]]
*[[RasMol]]
*Samson, see [[Sculpting protein conformations]].
*[[Swiss-PDBViewer = DeepView]]
**[[DeepView/Mutating Amino Acids]]

===EMail List===
*[[Proteopedia:Email list]]

===Meta Pages===
====Help====


*[[User:Eric Martz/Getting email from Proteopedia]]

*[[Help:Color Keys]]
*[[Help:Coloring text]]
*[[Help:Copying FirstGlance Scenes into Proteopedia]]
*[[Help:Editing]]
*[[Help:Getting Started in Proteopedia]]
*[[Help:How to Insert a ConSurf Result Into a Proteopedia Green Link]]
*[[Help:Language Translation]]
*[[Help:Making animations for Powerpoint]]
*[[Help:Plain text editors]]
*[[Help:Protected Pages]]
*[[Help:Quiz]]
*[[Help:Sandboxes]]
*[[Help:Snapshots]]
*[[Help:Uploading molecules]]

====Proteopedia====
*Mugs and T-Shirts: I created these products and set up the non-profit store at [http://www.cafepress.com/molviz4 cafepress.com/molviz4].
*[[News]] (disambiguation)
*[[Proteopedia:About]]
*[[Proteopedia:Guidelines for Ethical Writing]] was started by Jaime Prilusky. I added the sections on ''Content Attribution'' and ''Images''.
*[[User:Eric Martz/Proteopedia:Introduction]]
*[[Proteopedia:Languages]]
*[[Proteopedia:Namespaces]]
*[[Proteopedia:News]]
*[[Proteopedia:Overview]] <- [[Introduction to Proteopedia]]
*[[Proteopedia:Policy]]
*[[:Proteopedia:Problems]]
*[[Proteopedia:Scrapbook]]
*[[Proteopedia:Subdirectories]]
*[[Proteopedia:Supplementary materials]]
*[[Proteopedia:Topic Pages]]
*[[Proteopedia:What's New]] <- [[What's New?]], [[What's New]], [[what's new]], [[What's New in Proteopedia?]]
*[[:Proteopedia:Wishlist]]

====Proteopedia Pages Using Jmol Color Key Legends====
*[[Gramicidin Channel in Lipid Bilayer]]
*[[Metal-Ligand Polyhedra]]

{{Clear}}
===Mediawiki===
*[[Special:Prefixindex/Mediawiki:]]
*[[Special:Prefixindex/Mediawiki:Sat-tooltip]]

===Templates===
To find all templates contributed by a user, at the user's page, click User contributions (at left), then set the namespace to Templates.

*[[Template:Article_under_development]]
*[[Template:Button Toggle Animation]] used at [[Lac repressor]] and [[Template:Button Toggle Animation2]] generally more useful.
*[[Template:Chemical Components]]

<hr>
=====Color Keys=====
*[[Template:ColorKey_ConSurf]]
*[[Template:ColorKey_N2CRainbow]]
**Example of use: [[NMR_Ensembles_of_Models#Display_of_NMR_Models_by_Proteopedia]]
*The Templates used on the [[DRuMS]] and [[Help:Color Keys]] pages. All begin "Template:ColorKey".

<hr>
*[[Template:COVID Validation]]
*[[Template:EEEV]] and [[Template:EEEV-slab]]

<hr>
=====Green Links=====
*[[Template:Green_links_zoom]] See also adaptation emphasizing rotation of a morph at [[SARS-CoV-2_protein_S_activation_by_furin]]
*[[Template:ClickGreenLinks]]

<hr>
*[[Template:Homology Modeling Intro]]
*[[Template:Jmol application instructions]]
*[[Template:Martz email‎]]
*[[Template:Molecular Playground animation description]]
*[[Template:MP masthead]]
*[[Template:Murthy_fraud]]
*[[Template:PDBMapViewers]]
*[[Template:Possible_fraud]]
*[[Template:Protected page banner]]
**Example of use: [[User:Karl Oberholser/Ramachandran Plots]]
*[[Template:Sandbox Reserved Eric Martz]]
*[[Template:Sandbox Reserved Eric Martz 2]]
*[[Template:Sandbox Reserved Eric Martz 3]]
*[[Template:Theoretical model]]
*[[Template:Unsigned applets]]

==Pages by Others That I Especially Like==
This is not a complete list -- it is a just a few that I want to be able to find easily in case I forget.

* [[Ozonolysis]]
* [[2fbw]] has a comment (correction) by a user, illustrating how a banner alerts users about comments in the '''discussion''' tab.
* [[Proteopedia:Comments on Published Structures]]

==Workshops==
* [http://workshops.molviz.org One-day courses] in molecular visualization and structural bioinformatics for researchers and educators.

==Principal Author or Architect of (Elsewhere):==
* [http://firstglance.jmol.org FirstGlance in Jmol], a general-purpose molecular visualization tool which has been adopted by [http://www.nature.com/nature ''Nature''] (see the ''3D View'' links), [http://consurf.tau.ac.il the ConSurf Server], and [http://firstglance.jmol.org/adoption.htm other journals and structural bioinformatics servers]. Available 2005-present.
* Visualization for the [http://consurf.tau.ac.il the ConSurf Server] developed by Nir Ben-Tal, Fabian Glaser, Elana Erez and others, which colors amino acids by evolutionary conservation, completely automatically. Available 2002-present.
* [http://top5.molviz.org Top Five 3D Molecular Visualization Technologies for the Rest Of Us]. Page available 2007-present.
* [http://molviz.org MolviZ.Org] with tutorials in Jmol and molecular visualization resources for educators and students. Included is a [http://dna.molviz.org DNA Structure Tutorial] started in 1996, and now (in collaboration with [http://biomodel.uah.es/personal/inicio.htm Angel Herráez]) available in 5 languages.
* [[World Index of BioMolecular Visualization Resources]]. Available 2000-2012.
* [http://atlas.proteinexplorer.org Atlas of Macromolecules]. Available 2002-present.
* With [http://bip.weizmann.ac.il/staff/jaime_prilusky.html Jaime Prilusky], the [http://pdblite.org PDB Lite] search interface for students and beginners to find published macromolecular models. Available 1998-2010 (decommisioned).
* An incomplete [http://history.molviz.org History of Macromolecular Visualization] which includes a list of the earliest macromolecules solved by X-ray crystallography. Available 1997-present.
* [http://www.bioinformatics.org/mailman/listinfo/molvis-list molvis-list], founded in 1995 as the ''RasMol List''. Maintained largely by [http://molvisions.com Tim Driscoll/molvisions.com] since 2004.

And in an earlier era

* [http://proteinexplorer.org Protein Explorer] 1998-present.
* [http://rasmol.molviz.org The RasMol Classic Site] (formerly the ''RasMol Home Page'') founded 1996. (The current RasMol Home Page is at [http://rasmol.org RasMol.Org] by Herbert Bernstein, available since 1999.)

==Personal Quicklinks==
===Help===
*[[Special:Prefixindex]]
*<span style="font-size:150%">Samatey Group</span>
*<nowiki>{{Clear}}</nowiki>
*<nowiki><table align="right" width="" style="margin: 10px 10px;"><tr><td>[[Image:]]</table></table><tr><td>Caption</td></tr></table></nowiki>
*<nowiki>[[Image:wiki.png|frame|Wikipedia Encyclopedia]]</nowiki>
*[[Help:Editing]]
*[http://en.wikipedia.org/wiki/Help:Wiki_markup#Images Images: Basic Markup]   /   [http://en.wikipedia.org/wiki/Wikipedia:Extended_image_syntax Full Image Syntax]
*[http://en.wikipedia.org/wiki/Help:Table Tables]
*[[Proteopedia:Cookbook]]<small>
**Rectangular Jmol
**Image Maps
**Theoretical Model Template
**Floating Quote Box
**Links in Applet Caption
**Flash .swf</small>
*[[Template:Button_Toggle_Animation]]
*[[User:Eric Martz/Getting email from Proteopedia]]

===PDB Examples===
* Sites (after 2nd remediation): [[1uu1]] (AC1); [[1fws]] (AC1-6); [[1sid]] (AC1-9, BC1-9, all "binding sites"); [[1pop]] (AC1-AC9, BC1-BC9, CC1-CC6 all "binding sites" + CAT "CAT"); [[1zzz]] (CAT "Active Site");

===Files Uploaded===

*[http://proteopedia.org/wiki/index.php?limit=100&title=Special%3AContributions&contribs=user&target=Eric+Martz&namespace=6&year=&month=-1 Files Uploaded by Eric Martz]

===Sandboxes Reserved for Teaching===
*Created by Eric: 1-161
*[[Template:Sandbox Reserved Eric Martz]] [1-40] 1-10 May-July 2015 Osaka Univ
**Formerly 1-40 May-July 2014 Osaka Univ
**Formerly May-July 2013 Osaka Univ
**Formerly May-July 2012 Osaka Univ
**Formerly May-July 2011 Osaka Univ
**Formerly Apr-Jun 2010 Osaka Univ
*[[Template:Sandbox Reserved Eric Martz 2]] 41-100 Jan-Mar 2011 UMass
**Formerly 41-100 Feb-Mar 2010 Israel and extra 151-161
*[[Template:Sandbox Reserved Eric Martz 3]] [101-150] 101-125 May-July 2015 Okinawa Inst Sci Tech, Samatey
**Formerly Oct-Dec 2013 UMass Chem-Bio Interface Thompson
**Formerly May-Jul 2010 UMass
*[[Template:Sandbox Reserved Eric Martz 4]]

===Sandboxes for Collaborations===
*[[Sandbox Eric Martz]] (not protected) DeShais Collaboration
*[[Sandbox2 Eric Martz]] (not protected) ConSurfDB Collaboration
*[[Sandbox3 Eric Martz]] (not protected) (deleted; was Samatey)
*[[Sandbox4 Eric Martz]] (not protected) (available)
*[[Sandbox 5 Eric Martz]] (not protected) Heme Morph (Prilusky)
*[[Sandbox6 Eric Martz]] (not protected) Penghua Wang cas pa se 12
*[[Sandbox7 Eric Martz]] (not protected) (available)

===Sandboxes: Protected===
*[[User:Eric Martz/Sandbox]] Movie tests
*[[User:Eric Martz/Sandbox 0]] Knots in Proteins - see Methods in Sandbox 11
*[[User:Eric Martz/Sandbox 2]] FGiJ state script -> Proteopedia
*[[User:Eric Martz/Sandbox 3]] '''Miniprotein & microprotein notes'''
*[[User:Eric Martz/Sandbox 4]] Running state scripts for virus capsids and large assemblies
*[[User:Eric Martz/Sandbox 5]] Caption tests
*[[User:Eric Martz/Sandbox 6]] H274Y Tamiflu resistance mutation in N1
*[[User:Eric Martz/Sandbox 7]] PyMOL translator notes
*[[User:Eric Martz/Sandbox 8]] Water
*[[User:Eric Martz/Sandbox 9]] Tunnel
*[[User:Eric Martz/Sandbox 10]] hbonds
*[[User:Eric Martz/Sandbox 11]] knot methods
*[[User:Eric Martz/Sandbox 12]] links that perform searches
*[[User:Eric Martz/Sandbox 13]] Sequence Alignment Tools
*[[User:Eric Martz/Sandbox 14]] '''Jmol 12.2 Tests'''
*[[User:Eric Martz/Sandbox 15]] Ramachandran references
*[[User:Eric Martz/Sandbox 16]] PNGJ & caption SAT tests
*[[User:Eric Martz/Sandbox 17]] More PNGJ & caption SAT tests
*[[User:Eric Martz/Sandbox 18]] Saving from SAT removes FILTER command
*[[User:Eric Martz/Sandbox 19]] PACUPP analysis of porin
*[[User:Eric Martz/Sandbox 20]] '''Available'''
*[[User:Eric Martz/Sandbox 21]] '''Available'''
*[[User:Eric Martz/Sandbox 22]] '''Available'''

*[[User:Eric Martz/liveConnect Test]] hyperlink to javascript applet.script(...): HTML not interpreted

===Workbenches===
*[http://www.proteopedia.org/wiki/index.php?title=Special%3APrefixindex&from=User%3AEric+Martz%2FWorkbench&namespace=0 All Eric Martz Workbenches] (search using Prefixindex)
*[[User:Eric Martz/Workbench/AccountManagement]]
*[[User:Eric Martz/Workbench tests]]
*[[User:Eric Martz/Workbench/Workbench01]]
*[[User:Eric Martz/Workbench 02]] is for testing read access to users given permission.

===Collaborations===

====Samatey====
*[[Samatey]]
*[[Fadel_A._Samatey_Group]]
**[[Fadel A. Samatey Group (Japanese)]]
*'''[[User:Fadel A. Samatey]]''' has links to Samatey Workbenches
*[[User:Fadel_A._Samatey/FlhBc_I]] <- [[Samatey/1]] was not used in Acta Cryst D paper.
*[[User:Fadel_A._Samatey/FlgA_I]] <- [[Samatey/2]] linked in paper in SciRep.
*[[User:Fadel A. Samatey/FlgE I]] <- [[Samatey/3]] linked in paper in SciRep.
*[[User:Fadel A. Samatey/FlgE II/Complete Flagellar Hook Structure]] <- [[Samatey/4]] linked in paper in NatComm.
*[[Image:3b0z-all-chain-a.pdb.gz]]

====Malvankar Collaborations====
*[[User:Nikhil Malvankar]]
*[[Malvankar]]
*[[User:Nikhil Malvankar/Geobacter pilus]] <- [[Malvankar/1]]
*[[User:Nikhil Malvankar/Cytochrome nanowires]] <- [[Malvankar/2]]
*[[User:Nikhil_Malvankar/Geobacter_pilus_structure_and_function]] <- [[Malvankar/3]]

====Ke Xiao Collaborations====
*[[User:Ke_Xiao]]
*[[Ke_Xiao]]
*[[User:Ke_Xiao/Workbench_1]] -> [[Ke_Xiao/1]] -> [[User:Ke Xiao/Geobacter pilus models]]

===Protected Topic Pages===
*[[User:Eric Martz/Cavities tests]]
*[[User:Eric Martz/Entertaining PDB codes]] (amusing, humor)
*[[User:Eric Martz/Remarkable Structures]]
*[[User:Eric Martz/Nucleosomes]] (cf. [[Nucleosomes]])
*[[User:Eric Martz/Introduction to Structural Bioinformatics]] and [[User:Eric Martz/Introduction to Structural Bioinformatics I|2012]]
*[[User:Eric Martz/Virus capsid resources]]

*[[User:Eric Martz/Molecular Playground/Tamiflu]]
*[[User:Eric Martz/Molecular Playground/HIVDrug]]
*[[User:Eric Martz/Molecular Playground/Authoring]]

*[[User:Eric Martz/5eon]] cf. pili

===All Protected Pages===
*[[Special:Prefixindex/User:Eric_Martz]]
*[http://proteopedia.org/wiki/index.php?title=Special:Contributions&limit=500&contribs=user&target=Eric+Martz&namespace=2 Search for User:Eric Martz in User Namespace]

===Other Quicklinks===
*[[Special:Wantedpages]]

===Personal To Do List===
<font color="red">
*Knots
</font>
====Pages Needing Repairs====
*[[Lac repressor]] some scenes broken
*[[Structural alignment tools]]: the morph green link hangs JSmol (2/2021) but morph green links work on other pages (tested: Lac repressor, recovering, mechanosensitive, avian influ.)

User talk:Masaki Unno

2026-10-02T13:20:31Z

Eric Martz: Welcome!

User:Masaki Unno

2026-10-02T13:20:31Z

Eric Martz: Creating user page for new user.

Position: Professor
Institution (NO ABBREVIATIONS): Ibaraki University
City: Hitachi
State/Province: Ibaraki
Country: Japan
Field of Expertise or Study: Structural Biology
ORCID ID: 0000-0002-4975-5696

AlphaFold

2026-09-29T14:52:26Z

Eric Martz:

[[Image:Hassabis_Demis.jpg|300px|right|thumb| Demis Hassabis - DeepMind]]
[[Image:Jumper_John.jpg|300px|right|thumb| John Jumper - DeepMind]]
<table style="background-color:#ffffb0;"><tr><td>
October 2024: David Baker, Demis Hassabis, and John M. Jumper share the [[Nobel_Prizes_for_3D_Molecular_Structure#2020-2029|Nobel Prize in Chemistry]], Baker for "computational protein design", Hassabis and Jumper for "protein structure prediction", namely, AlphaFold.
* [https://www.youtube.com/watch?v=cx7l9ZGFZkw 22 min video] explaining their contributions.
* [https://www.youtube.com/watch?v=g96tXNwrYXc 9 min video] of David Baker explaining his protein design work.
* [https://www.youtube.com/watch?v=SdxOouXsaxc 4 min video] of Demis Hassabis and John Jumper reacting to their Nobel Prize.
The [https://www.nobelprize.org/prizes/physics/2024/press-release/ 2024 Nobel Prize in Physics went to John J. Hopfield and Geoffrey E. Hinton] for machine learning with neural networks, technology that underlies the prizewinning work in Chemistry.
</td></tr></table>

In 2020, the '''AlphaFold2'''<ref name="senior202001">PMID: 31942072</ref><ref name="alphafoldwikipedia">[https://en.wikipedia.org/wiki/AlphaFold AlphaFold] at Wikipedia.</ref> system of [https://deepmind.com DeepMind]<ref name="deepmindblog">[https://deepmind.com/blog/article/alphafold-a-solution-to-a-50-year-old-grand-challenge-in-biology AlphaFold: a solution to a 50-year-old grand challenge in biology], DeepMind Blog, November 30, 2020.</ref><ref name="deepmindwikipedia">[https://en.wikipedia.org/wiki/DeepMind DeepMind] at Wikipedia.</ref> demonstrated a '''major breakthrough'''<ref name="alquraishi">[https://moalquraishi.wordpress.com/2020/12/08/alphafold2-casp14-it-feels-like-ones-child-has-left-home/ AlphaFold2 @ CASP14: “It feels like one’s child has left home.”] by Mohammed AlQuraishi, December 8, 2020.</ref><ref name="casppressrelease">[https://predictioncenter.org/casp14/doc/CASP14_press_release.html Artificial intelligence solution to a 50-year-old science challenge could ‘revolutionise’ medical research], CASP Press Release, November 30, 2020.</ref><ref name="callaway" /><ref name="helliwell">[https://www.iucr.org/news/newsletter/volume-28/number-4/deepmind-and-casp14 DeepMind and CASP14] by John R. Helliwell, International Union of Crystallography Newsletter, December 4, 2020.</ref>. At [[Theoretical_models#2020:_CASP_14|CASP14]], AlphaFold2 was far better able, among over 100 competing groups, to '''predict structures, including sidechain positions''', so close to the subsequently revealed X-ray crystallographic structures as to differ by little more than the differences between two independently-determined X-ray structures of the same molecule. It did this for about two-thirds of the targets in the competition. AlphaFold2 has been hailed as '''largely solving the protein structure prediction problem for single-chain proteins'''<ref name="alquraishi" /><ref name="casppressrelease" /><ref name="callaway">PMID: 33257889</ref><ref name="helliwell" />. "Never in my life had I expected to see a scientific advance so rapid." said Mohammed AlQuraishi of Columbia University<ref name="alquraishi" />. But consider also "The joys and perils of AlphaFold"<ref name="perils">PMID: 34668287</ref>.

In 2022, at [[CASP]] 15, AlphaFold2 continued to outperform all other methods in the majority of cases (see a summary of results at [[Theoretical_models#2022:_CASP_15|Theoretical models]]).

In September, 2023, John Jumper and Demis Hassabis received the [https://laskerfoundation.org/winners/alphafold-a-technology-for-predicting-protein-structures Lasker Award] for revolutionizing protein structure prediction<ref name="lasker-scientist">[https://www.the-scientist.com/news/lasker-award-for-revolutionizing-protein-structure-predictions-71386 Lasker Award for Revolutionizing Protein Structure Predictions], Laura Tran, <i>The Scientist</i>, September, 2023.</ref><ref name="lasker-nature">PMID: 37752227</ref>.

<table style="background-color:#e0ffe0;border:1px solid black;font-size:120%;"><tr><td>
If you want an AlphaFold-predicted structure for a protein sequence:
* If a prediction is already in the [[#AlphaFold Database of Predictions|AlphaFold Database]], simply download it. Limited to single chain proteins without ligands.
* Otherwise, and for multiple chain (protein/nucleic acid) structures with ligands, follow [[How to predict structures with AlphaFold]].
* Dropping the predicted model into [http://FirstGlance.Jmol.Org FirstGlance in Jmol] will automatically '''color it by estimated reliability per residue'''. Examples: [http://bioinformatics.org/molvis/images/firstglance-with-alphafold.png Snapshot], [https://molviz.org/firstglance/fgij/fg.htm?mol=AFDB-Q9AY27-F1-model_v1.pdb Interactive].
</td></tr></table>

2021 Resources: [For more recent resources and servers, see [[How to predict structures with AlphaFold]].]
* See [https://www.ebi.ac.uk/training/online/courses/alphafold AlphaFold A practical Guide] Superb EMBL-EBI Interactive online tutorial on AlphaFold2 (~3 hours)
*See short [https://mediasite.embl.de/Mediasite/Play/a320afff218d4a3cbad6ea6eca5212931d superb lecture] on AlphaFold by the CEO of ''DeepMind'', '''Dennis Hassabis''', that was given at the EMBL, Heidelberg, on 3-Feb-2022, entitled '''Using AI to accelerate scientific discovery'''.
*see [https://youtu.be/UqeQfRDA8Yk EMBL-EBI-Training Video] six superb short talks on AlphaFold2
*See [[Theoretical_models#2020:_CASP_14]] for more about the initial success at CASP14, and the reactions to it.
*[[Theoretical_models#AlphaFold2_Methods|AlphaFold2 Methods]]
*[[AlphaFold2_examples_from_CASP_14]] describes a detailed analysis of two of the CASP14 predictions.

==AlphaFold Database of Predictions==

In 2023, the free [https://alphafold.ebi.ac.uk/ AlphaFold Database] has been expanded to >200 million structures. Proteins in
[http://uniprot.org UniProt] now link to the AlphaFold models in the Structure section. For an overview of which proteins are and are not in the AlphaFold Database, see ''Which proteins are included?'' in the FAQ at the main page of AlphaFold Database.

In July, 2021, DeepMind made available over 300,000 structure predictions from amino acid sequences in their free [https://alphafold.ebi.ac.uk/ AlphaFold DB]<ref name="deepminddb">[https://deepmind.com/research/case-studies/alphafold#a_treasure_trove We’ve made AlphaFold predictions freely available to anyone in the scientific community] at DeepMind.com (date of release not specified, approximately July 2021).</ref><ref name="afdbebi">[https://www.ebi.ac.uk/pdbe/about/news/alphafold%E2%80%99s-protein-structure-predictions-now-available-explore AlphaFold’s protein structure predictions now available to explore] at the European Bioinformatics Institute, July 23, 2021.</ref><ref name="impacts">[https://www.embl.org/news/science/alphafold-potential-impacts/ Great expectations – the potential impacts of AlphaFold DB] at the European Bioinformatics Institute, July 22, 2021</ref><ref name="human">[https://www.embl.org/news/science/alphafold-database-launch/ DeepMind and EMBL release the most complete database of predicted 3D structures of human proteins] at the European Bioinformatics Institute, July 22, 2021.</ref>. These predictions include nearly all ~20,000 proteins in the human proteome, 36% with very high confidence, and another 22% with high confidence<ref name="human" /><ref name="human-nature">PMID: 34293799</ref>. Also included are ''E. coli'', fruit fly, mouse, zebrafish, malaria parasite and tuberculosis bacteria<ref name="human" />. Limitations of these predictions were enumerated<ref name="impacts" /><ref name="perils" />, including:
* Inability to predict protein-protein or protein-DNA/RNA/ligand complexes. [[#RoseTTAFold]] and AlphaFold both claim progress on predicting protein-protein complexes.
* Does not predict ligands, cofactors, metals, ions, glycosylation, etc. (Efforts to extend to such: see [[#Ligands: AlphaFill|AlphaFill below]]; and [https://www.nature.com/articles/s41594-021-00680-9 glycolsylations].)
* Does not deal with conformational dynamics.
* Does not predict [[Intrinsically Disordered Protein|intrinsically unstructured]] segments.
* Does not predict the folding pathway.
* Has not been trained to predict structural consequences of '''point mutations'''.

Nevertheless, these predictions have many potential benefits<ref name="impacts" />, including:
* Simplifying [[X-ray crystallography]] by enabling solution of the phase problem by molecular replacement using the predicted model.
* Assisting crystallographers in defining [[domain]] boundaries in order to crystallize domains when crystallization of full length proteins is problematic.
* Helping to interpret >5,000 [[cryo-EM]] maps previously deposited in the [[EMDB]] that could not be interpreted as atomic models, as well as helping to interpret lower resolution EM maps as atomic models.

===Ligands: AlphaFill===
The AlphaFold Database has been enhanced by "transplanting" ligands from empirical structures similar to predicted structures. Results are in the [http://alphafill.eu AlphaFill Database] ([https://biorxiv.org/cgi/content/short/2021.11.26.470110 preprint]). The authors caution
<blockquote>
"AlphaFill models are not meant or suitable for precise quantification of interactions between the transferred ligand(s) and the protein (e.g. hydrogen bonds, π-π or cation-π interactions, van der Waals interactions, hydrophobic interactions, halogen bonds). These require coordinate precision that is not provided by either the AlphaFold or the AlphaFill models at the current stage, and the models should only be interpreted in a qualitative manner."
</blockquote>

==AlphaFold published July 2021==
[For recent prediction servers, see [[How to predict structures with AlphaFold]].]

AlphaFold was published in July, 2021<ref name="af2021">PMID: 34265844</ref>. Methods were described in considerable detail. The source code, trained weights, and inference script were made available under an '''open-source license'''. Structure prediction required about one GPU (Graphics Processing Unit) minute per model of about 384 amino acids.

Impressively, AlphaFold had remarkable success predicting a set of 10,795 protein chain structures (filtered for high reliability, lengths restricted to 80-1,400 residues) published in the [[PDB]] after AlphaFold's training set<ref>The training set cutoff was 2018/04/30. The test set was obtained between then and 2021/02/15.</ref>. Overall alpha carbon accuracy had a median of 1.46 Å [[Calculating GDT TS|RMSD]] at 95% coverage. The majority of chain structures were predicted with full-chain alpha carbon RMSD values <2 Å. About 25% were predicted with RMSD >4 Å.

Importantly, each prediction comes with a confidence score that reliably predicts the accuracy of the predicted structure.

Accurate prediction of sidechains required accurate prediction of the main chain. Accurate prediction required a multiple sequence alignment depth >~30 sequences, with a depth of ~100 sequences being adequate.

==Free AlphaFold-based Servers==

<table style="background-color:#e0ffe0;border:1px solid black;font-size:120%;"><tr><td>
If you want an AlphaFold-predicted structure for a protein sequence:
* If a prediction is already in the [[#AlphaFold Database of Predictions|AlphaFold Database]], simply download it. Limited to single chain proteins without ligands.
* Otherwise, and for multiple chain (protein/nucleic acid) structures with ligands, follow [[How to predict structures with AlphaFold]].
* Uploading the predicted PDB file to [http://FirstGlance.Jmol.Org FirstGlance in Jmol] will automatically '''color it by estimated reliability per residue'''. Examples: [http://bioinformatics.org/molvis/images/firstglance-with-alphafold.png Snapshot], [http://firstglance.jmol.org/fg.htm?mol=AF-Q9AY27-F1-model_v1.pdb Interactive].
</td></tr></table>

===RoseTTAFold===

Also in July, 2021, Minkyung Baek and a large team in the [https://www.bakerlab.org/ group of David Baker] published their '''RoseTTAFold''' employing a three-track network, based in part on methods inspired by AlphaFold but not yet fully-detailed by DeepMind. They reported "accuracies approaching those of DeepMind in CASP14"<ref name="baek1">PMID: 34282049</ref>. At the time of its release in July, 2021, it had outperformed all other available structure prediction ''servers''<ref name="baek1" />.

The [https://robetta.bakerlab.org/ RoseTTAFold Server] was made freely available. (Open the ''Structure Prediction'' menu at the top and choose ''Submit''. At the form, be sure to check ''RoseTTAFold'' before submitting your job).

===AlphaFold Colab===
Google provides "Colaboratories" (Colabs). A Colab "allows anybody to write and execute arbitrary python code through the browser, and is especially well suited to machine learning, data analysis and education"<ref name="colabfaq">[https://research.google.com/colaboratory/faq.html Collaboratory FAQ] at Google.</ref>.

DeepMind has provided an [https://colab.research.google.com/github/deepmind/alphafold/blob/main/notebooks/AlphaFold.ipynb Alphafold Colab] that uses a "slightly simplified" version of AlphaFold version 2.0: "While accuracy will be near-identical to the full AlphaFold system on many targets, a small fraction have a large drop in accuracy due to the smaller MSA and lack of templates.". The AlphaFold Colab is '''free to use'''. The code is executed in a virtual machine private to your account, and data are stored on Google Drive. Nothing is installed on your computer; "everything happens in the cloud on Google Colab"<ref name="alphafoldcolab">[https://colab.research.google.com/github/deepmind/alphafold/blob/main/notebooks/AlphaFold.ipynb Alphafold Colab].</ref> See [[How to predict structures with AlphaFold]].

For those unfamiliar with Colabs, the user interface may look unfamiliar, but the instructions are clear and straightforward to use. The mentions of "Runtime -> Run after" refer to the Runtime pull-down menu at the very top of the page. Getting a result may take several hours.

===ColabFold: AlphaFold2 with MMSeqs2===

[https://colab.research.google.com/github/sokrypton/ColabFold/blob/main/AlphaFold2.ipynb A colab by Sergey Ovchinnikov, Milot Mirdita and Martin Steinegger]. In their [https://www.biorxiv.org/content/10.1101/2021.08.15.456425v1 accompanying publication] they state:
<blockquote>
"MMseqs2’s MSAs [multiple sequence alignments] produce more accurate predictions while being ~16 faster compared to the AlphaFold2’s MSA stage. ColabFold also offers many advanced features, such as homo- and hetero-complex modeling and exposes AlphaFold2 internals."
</blockquote>

===Current offerings via Colab===

Work is ongoing and other offerings are now available on Colab for RoseTTAFold and AlphaFold2 besides the ones detailed above. This summary guide & video should help in choosing how to analyze your proteins of interest:

- [https://github.com/sokrypton/ColabFold#making-protein-folding-accessible-to-all-via-google-colab A Guide to the free RoseTTAFold and AlphaFold 2 Colab notebooks]

- ColabFold: A [https://www.youtube.com/watch?v=Rfw7thgGTwI video covering an overview, comparison of some of the methods and how people are already extending them, how to submit and interpret, and a tutorial on how to use AlphaFold2 Colab] is available. The video was recorded on August 4th, 2021 presented by Sergey Ovchinnikov and Martin Steinegger, hosted by Chris Bahl for the Boston Protein Design and Modeling Club

==Advances since 2021==
*See a list of newer servers at [[How to predict structures with AlphaFold]].
*RoseTTAFoldNA<ref>PMID: 37996753</ref> offers a leap forward in predicting structures of complexes of proteins and nucleic acids, but in November 2023 is not yet available as a free server.

==See Also==
*[[How to predict structures with AlphaFold]].
*[[AlphaFold/Index]], a list of pages in Proteopedia about Alphafold.
*[[How To Find A Structure]] covers both [[empirical models]] and the advantages of comparing them with AlphaFold models due to [[missing residues and incomplete sidechains]] prevalent in empirical models.

==References==
<references />

==Further reading==

* '''AlphaFold protein structure predictions - a step change for biology.'''
: (Report by Oana Stroe, Senior Communications Officer at EMBL-EBI. 28 July 2021 at [https://bit.ly/2UZREPx FEBS Network])
: Sameer Velankar and Gerard Kleywegt, from the Protein Data Bank in Europe, and Alex Bateman, Head of Protein Sequence Resources, all at EMBL’s European Bioinformatics Institute (EMBL-EBI), explore the research avenues opened up by the AlphaFold database and explain the method's limitations.

* '''A structural biology community assessment of AlphaFold 2 applications.'''
: Akdel et al., 2021
: https://biorxiv.org/cgi/content/short/2021.09.26.461876
: Several findings:
:: AlphaFold 2 can often predict the correct homo-oligomer structure when given the correct oligomeric state (number of copies in complex); however, it's not always able to predict the correct oligomeric state ''a priori''.
:: "AF2 models can be used across diverse applications equally well compared to experimentally determined structures, when the confidence metrics are critically considered."

* '''Protein complex prediction with AlphaFold-Multimer '''
: Evans et al., 2021
: https://www.biorxiv.org/content/10.1101/2021.10.04.463034
: Highlights:
:: Fine tuned Alphafold 2 model for protein interaction predictions.
:: "The source code and weights for the trained models will be made available shortly."

AlphaFold

2026-09-29T14:48:25Z

Eric Martz:

[[Image:Hassabis_Demis.jpg|300px|right|thumb| Demis Hassabis - DeepMind]]
[[Image:Jumper_John.jpg|300px|right|thumb| John Jumper - DeepMind]]
<table style="background-color:#ffffb0;"><tr><td>
October 2024: David Baker, Demis Hassabis, and John M. Jumper share the [[Nobel_Prizes_for_3D_Molecular_Structure#2020-2029|Nobel Prize in Chemistry]], Baker for "computational protein design", Hassabis and Jumper for "protein structure prediction", namely, AlphaFold.
* [https://www.youtube.com/watch?v=cx7l9ZGFZkw 22 min video] explaining their contributions.
* [https://www.youtube.com/watch?v=g96tXNwrYXc 9 min video] of David Baker explaining his protein design work.
* [https://www.youtube.com/watch?v=SdxOouXsaxc 4 min video] of Demis Hassabis and John Jumper reacting to their Nobel Prize.
The [https://www.nobelprize.org/prizes/physics/2024/press-release/ 2024 Nobel Prize in Physics went to John J. Hopfield and Geoffrey E. Hinton] for machine learning with neural networks, technology that underlies the prizewinning work in Chemistry.
</td></tr></table>

In 2020, the '''AlphaFold2'''<ref name="senior202001">PMID: 31942072</ref><ref name="alphafoldwikipedia">[https://en.wikipedia.org/wiki/AlphaFold AlphaFold] at Wikipedia.</ref> system of [https://deepmind.com DeepMind]<ref name="deepmindblog">[https://deepmind.com/blog/article/alphafold-a-solution-to-a-50-year-old-grand-challenge-in-biology AlphaFold: a solution to a 50-year-old grand challenge in biology], DeepMind Blog, November 30, 2020.</ref><ref name="deepmindwikipedia">[https://en.wikipedia.org/wiki/DeepMind DeepMind] at Wikipedia.</ref> demonstrated a '''major breakthrough'''<ref name="alquraishi">[https://moalquraishi.wordpress.com/2020/12/08/alphafold2-casp14-it-feels-like-ones-child-has-left-home/ AlphaFold2 @ CASP14: “It feels like one’s child has left home.”] by Mohammed AlQuraishi, December 8, 2020.</ref><ref name="casppressrelease">[https://predictioncenter.org/casp14/doc/CASP14_press_release.html Artificial intelligence solution to a 50-year-old science challenge could ‘revolutionise’ medical research], CASP Press Release, November 30, 2020.</ref><ref name="callaway" /><ref name="helliwell">[https://www.iucr.org/news/newsletter/volume-28/number-4/deepmind-and-casp14 DeepMind and CASP14] by John R. Helliwell, International Union of Crystallography Newsletter, December 4, 2020.</ref>. At [[Theoretical_models#2020:_CASP_14|CASP14]], AlphaFold2 was far better able, among over 100 competing groups, to '''predict structures, including sidechain positions''', so close to the subsequently revealed X-ray crystallographic structures as to differ by little more than the differences between two independently-determined X-ray structures of the same molecule. It did this for about two-thirds of the targets in the competition. AlphaFold2 has been hailed as '''largely solving the protein structure prediction problem for single-chain proteins'''<ref name="alquraishi" /><ref name="casppressrelease" /><ref name="callaway">PMID: 33257889</ref><ref name="helliwell" />. "Never in my life had I expected to see a scientific advance so rapid." said Mohammed AlQuraishi of Columbia University<ref name="alquraishi" />. But consider also "The joys and perils of AlphaFold"<ref name="perils">PMID: 34668287</ref>.

In 2022, at [[CASP]] 15, AlphaFold2 continued to outperform all other methods in the majority of cases (see a summary of results at [[Theoretical_models#2022:_CASP_15|Theoretical models]]).

In September, 2023, John Jumper and Demis Hassabis received the [https://laskerfoundation.org/winners/alphafold-a-technology-for-predicting-protein-structures Lasker Award] for revolutionizing protein structure prediction<ref name="lasker-scientist">[https://www.the-scientist.com/news/lasker-award-for-revolutionizing-protein-structure-predictions-71386 Lasker Award for Revolutionizing Protein Structure Predictions], Laura Tran, <i>The Scientist</i>, September, 2023.</ref><ref name="lasker-nature">PMID: 37752227</ref>.

<table style="background-color:#e0ffe0;border:1px solid black;font-size:120%;"><tr><td>
If you want an AlphaFold-predicted structure for a protein sequence:
* If a prediction is already in the [[#AlphaFold Database of Predictions|AlphaFold Database]], simply download it. Limited to single chain proteins without ligands.
* Otherwise, and for multiple chain (protein/nucleic acid) structures with ligands, follow [[How to predict structures with AlphaFold]].
* Dropping the predicted model into [http://FirstGlance.Jmol.Org FirstGlance in Jmol] will automatically '''color it by estimated reliability per residue'''. Examples: [http://bioinformatics.org/molvis/images/firstglance-with-alphafold.png Snapshot], [https://molviz.org/firstglance/fgij/fg.htm?mol=AF-Q9AY27-F1-model_v1.pdb Interactive].
</td></tr></table>

2021 Resources: [For more recent resources and servers, see [[How to predict structures with AlphaFold]].]
* See [https://www.ebi.ac.uk/training/online/courses/alphafold AlphaFold A practical Guide] Superb EMBL-EBI Interactive online tutorial on AlphaFold2 (~3 hours)
*See short [https://mediasite.embl.de/Mediasite/Play/a320afff218d4a3cbad6ea6eca5212931d superb lecture] on AlphaFold by the CEO of ''DeepMind'', '''Dennis Hassabis''', that was given at the EMBL, Heidelberg, on 3-Feb-2022, entitled '''Using AI to accelerate scientific discovery'''.
*see [https://youtu.be/UqeQfRDA8Yk EMBL-EBI-Training Video] six superb short talks on AlphaFold2
*See [[Theoretical_models#2020:_CASP_14]] for more about the initial success at CASP14, and the reactions to it.
*[[Theoretical_models#AlphaFold2_Methods|AlphaFold2 Methods]]
*[[AlphaFold2_examples_from_CASP_14]] describes a detailed analysis of two of the CASP14 predictions.

==AlphaFold Database of Predictions==

In 2023, the free [https://alphafold.ebi.ac.uk/ AlphaFold Database] has been expanded to >200 million structures. Proteins in
[http://uniprot.org UniProt] now link to the AlphaFold models in the Structure section. For an overview of which proteins are and are not in the AlphaFold Database, see ''Which proteins are included?'' in the FAQ at the main page of AlphaFold Database.

In July, 2021, DeepMind made available over 300,000 structure predictions from amino acid sequences in their free [https://alphafold.ebi.ac.uk/ AlphaFold DB]<ref name="deepminddb">[https://deepmind.com/research/case-studies/alphafold#a_treasure_trove We’ve made AlphaFold predictions freely available to anyone in the scientific community] at DeepMind.com (date of release not specified, approximately July 2021).</ref><ref name="afdbebi">[https://www.ebi.ac.uk/pdbe/about/news/alphafold%E2%80%99s-protein-structure-predictions-now-available-explore AlphaFold’s protein structure predictions now available to explore] at the European Bioinformatics Institute, July 23, 2021.</ref><ref name="impacts">[https://www.embl.org/news/science/alphafold-potential-impacts/ Great expectations – the potential impacts of AlphaFold DB] at the European Bioinformatics Institute, July 22, 2021</ref><ref name="human">[https://www.embl.org/news/science/alphafold-database-launch/ DeepMind and EMBL release the most complete database of predicted 3D structures of human proteins] at the European Bioinformatics Institute, July 22, 2021.</ref>. These predictions include nearly all ~20,000 proteins in the human proteome, 36% with very high confidence, and another 22% with high confidence<ref name="human" /><ref name="human-nature">PMID: 34293799</ref>. Also included are ''E. coli'', fruit fly, mouse, zebrafish, malaria parasite and tuberculosis bacteria<ref name="human" />. Limitations of these predictions were enumerated<ref name="impacts" /><ref name="perils" />, including:
* Inability to predict protein-protein or protein-DNA/RNA/ligand complexes. [[#RoseTTAFold]] and AlphaFold both claim progress on predicting protein-protein complexes.
* Does not predict ligands, cofactors, metals, ions, glycosylation, etc. (Efforts to extend to such: see [[#Ligands: AlphaFill|AlphaFill below]]; and [https://www.nature.com/articles/s41594-021-00680-9 glycolsylations].)
* Does not deal with conformational dynamics.
* Does not predict [[Intrinsically Disordered Protein|intrinsically unstructured]] segments.
* Does not predict the folding pathway.
* Has not been trained to predict structural consequences of '''point mutations'''.

Nevertheless, these predictions have many potential benefits<ref name="impacts" />, including:
* Simplifying [[X-ray crystallography]] by enabling solution of the phase problem by molecular replacement using the predicted model.
* Assisting crystallographers in defining [[domain]] boundaries in order to crystallize domains when crystallization of full length proteins is problematic.
* Helping to interpret >5,000 [[cryo-EM]] maps previously deposited in the [[EMDB]] that could not be interpreted as atomic models, as well as helping to interpret lower resolution EM maps as atomic models.

===Ligands: AlphaFill===
The AlphaFold Database has been enhanced by "transplanting" ligands from empirical structures similar to predicted structures. Results are in the [http://alphafill.eu AlphaFill Database] ([https://biorxiv.org/cgi/content/short/2021.11.26.470110 preprint]). The authors caution
<blockquote>
"AlphaFill models are not meant or suitable for precise quantification of interactions between the transferred ligand(s) and the protein (e.g. hydrogen bonds, π-π or cation-π interactions, van der Waals interactions, hydrophobic interactions, halogen bonds). These require coordinate precision that is not provided by either the AlphaFold or the AlphaFill models at the current stage, and the models should only be interpreted in a qualitative manner."
</blockquote>

==AlphaFold published July 2021==
[For recent prediction servers, see [[How to predict structures with AlphaFold]].]

AlphaFold was published in July, 2021<ref name="af2021">PMID: 34265844</ref>. Methods were described in considerable detail. The source code, trained weights, and inference script were made available under an '''open-source license'''. Structure prediction required about one GPU (Graphics Processing Unit) minute per model of about 384 amino acids.

Impressively, AlphaFold had remarkable success predicting a set of 10,795 protein chain structures (filtered for high reliability, lengths restricted to 80-1,400 residues) published in the [[PDB]] after AlphaFold's training set<ref>The training set cutoff was 2018/04/30. The test set was obtained between then and 2021/02/15.</ref>. Overall alpha carbon accuracy had a median of 1.46 Å [[Calculating GDT TS|RMSD]] at 95% coverage. The majority of chain structures were predicted with full-chain alpha carbon RMSD values <2 Å. About 25% were predicted with RMSD >4 Å.

Importantly, each prediction comes with a confidence score that reliably predicts the accuracy of the predicted structure.

Accurate prediction of sidechains required accurate prediction of the main chain. Accurate prediction required a multiple sequence alignment depth >~30 sequences, with a depth of ~100 sequences being adequate.

==Free AlphaFold-based Servers==

<table style="background-color:#e0ffe0;border:1px solid black;font-size:120%;"><tr><td>
If you want an AlphaFold-predicted structure for a protein sequence:
* If a prediction is already in the [[#AlphaFold Database of Predictions|AlphaFold Database]], simply download it. Limited to single chain proteins without ligands.
* Otherwise, and for multiple chain (protein/nucleic acid) structures with ligands, follow [[How to predict structures with AlphaFold]].
* Uploading the predicted PDB file to [http://FirstGlance.Jmol.Org FirstGlance in Jmol] will automatically '''color it by estimated reliability per residue'''. Examples: [http://bioinformatics.org/molvis/images/firstglance-with-alphafold.png Snapshot], [http://firstglance.jmol.org/fg.htm?mol=AF-Q9AY27-F1-model_v1.pdb Interactive].
</td></tr></table>

===RoseTTAFold===

Also in July, 2021, Minkyung Baek and a large team in the [https://www.bakerlab.org/ group of David Baker] published their '''RoseTTAFold''' employing a three-track network, based in part on methods inspired by AlphaFold but not yet fully-detailed by DeepMind. They reported "accuracies approaching those of DeepMind in CASP14"<ref name="baek1">PMID: 34282049</ref>. At the time of its release in July, 2021, it had outperformed all other available structure prediction ''servers''<ref name="baek1" />.

The [https://robetta.bakerlab.org/ RoseTTAFold Server] was made freely available. (Open the ''Structure Prediction'' menu at the top and choose ''Submit''. At the form, be sure to check ''RoseTTAFold'' before submitting your job).

===AlphaFold Colab===
Google provides "Colaboratories" (Colabs). A Colab "allows anybody to write and execute arbitrary python code through the browser, and is especially well suited to machine learning, data analysis and education"<ref name="colabfaq">[https://research.google.com/colaboratory/faq.html Collaboratory FAQ] at Google.</ref>.

DeepMind has provided an [https://colab.research.google.com/github/deepmind/alphafold/blob/main/notebooks/AlphaFold.ipynb Alphafold Colab] that uses a "slightly simplified" version of AlphaFold version 2.0: "While accuracy will be near-identical to the full AlphaFold system on many targets, a small fraction have a large drop in accuracy due to the smaller MSA and lack of templates.". The AlphaFold Colab is '''free to use'''. The code is executed in a virtual machine private to your account, and data are stored on Google Drive. Nothing is installed on your computer; "everything happens in the cloud on Google Colab"<ref name="alphafoldcolab">[https://colab.research.google.com/github/deepmind/alphafold/blob/main/notebooks/AlphaFold.ipynb Alphafold Colab].</ref> See [[How to predict structures with AlphaFold]].

For those unfamiliar with Colabs, the user interface may look unfamiliar, but the instructions are clear and straightforward to use. The mentions of "Runtime -> Run after" refer to the Runtime pull-down menu at the very top of the page. Getting a result may take several hours.

===ColabFold: AlphaFold2 with MMSeqs2===

[https://colab.research.google.com/github/sokrypton/ColabFold/blob/main/AlphaFold2.ipynb A colab by Sergey Ovchinnikov, Milot Mirdita and Martin Steinegger]. In their [https://www.biorxiv.org/content/10.1101/2021.08.15.456425v1 accompanying publication] they state:
<blockquote>
"MMseqs2’s MSAs [multiple sequence alignments] produce more accurate predictions while being ~16 faster compared to the AlphaFold2’s MSA stage. ColabFold also offers many advanced features, such as homo- and hetero-complex modeling and exposes AlphaFold2 internals."
</blockquote>

===Current offerings via Colab===

Work is ongoing and other offerings are now available on Colab for RoseTTAFold and AlphaFold2 besides the ones detailed above. This summary guide & video should help in choosing how to analyze your proteins of interest:

- [https://github.com/sokrypton/ColabFold#making-protein-folding-accessible-to-all-via-google-colab A Guide to the free RoseTTAFold and AlphaFold 2 Colab notebooks]

- ColabFold: A [https://www.youtube.com/watch?v=Rfw7thgGTwI video covering an overview, comparison of some of the methods and how people are already extending them, how to submit and interpret, and a tutorial on how to use AlphaFold2 Colab] is available. The video was recorded on August 4th, 2021 presented by Sergey Ovchinnikov and Martin Steinegger, hosted by Chris Bahl for the Boston Protein Design and Modeling Club

==Advances since 2021==
*See a list of newer servers at [[How to predict structures with AlphaFold]].
*RoseTTAFoldNA<ref>PMID: 37996753</ref> offers a leap forward in predicting structures of complexes of proteins and nucleic acids, but in November 2023 is not yet available as a free server.

==See Also==
*[[How to predict structures with AlphaFold]].
*[[AlphaFold/Index]], a list of pages in Proteopedia about Alphafold.
*[[How To Find A Structure]] covers both [[empirical models]] and the advantages of comparing them with AlphaFold models due to [[missing residues and incomplete sidechains]] prevalent in empirical models.

==References==
<references />

==Further reading==

* '''AlphaFold protein structure predictions - a step change for biology.'''
: (Report by Oana Stroe, Senior Communications Officer at EMBL-EBI. 28 July 2021 at [https://bit.ly/2UZREPx FEBS Network])
: Sameer Velankar and Gerard Kleywegt, from the Protein Data Bank in Europe, and Alex Bateman, Head of Protein Sequence Resources, all at EMBL’s European Bioinformatics Institute (EMBL-EBI), explore the research avenues opened up by the AlphaFold database and explain the method's limitations.

* '''A structural biology community assessment of AlphaFold 2 applications.'''
: Akdel et al., 2021
: https://biorxiv.org/cgi/content/short/2021.09.26.461876
: Several findings:
:: AlphaFold 2 can often predict the correct homo-oligomer structure when given the correct oligomeric state (number of copies in complex); however, it's not always able to predict the correct oligomeric state ''a priori''.
:: "AF2 models can be used across diverse applications equally well compared to experimentally determined structures, when the confidence metrics are critically considered."

* '''Protein complex prediction with AlphaFold-Multimer '''
: Evans et al., 2021
: https://www.biorxiv.org/content/10.1101/2021.10.04.463034
: Highlights:
:: Fine tuned Alphafold 2 model for protein interaction predictions.
:: "The source code and weights for the trained models will be made available shortly."

AlphaFold

2026-09-29T14:46:52Z

Eric Martz:

[[Image:Hassabis_Demis.jpg|300px|right|thumb| Demis Hassabis - DeepMind]]
[[Image:Jumper_John.jpg|300px|right|thumb| John Jumper - DeepMind]]
<table style="background-color:#ffffb0;"><tr><td>
October 2024: David Baker, Demis Hassabis, and John M. Jumper share the [[Nobel_Prizes_for_3D_Molecular_Structure#2020-2029|Nobel Prize in Chemistry]], Baker for "computational protein design", Hassabis and Jumper for "protein structure prediction", namely, AlphaFold.
* [https://www.youtube.com/watch?v=cx7l9ZGFZkw 22 min video] explaining their contributions.
* [https://www.youtube.com/watch?v=g96tXNwrYXc 9 min video] of David Baker explaining his protein design work.
* [https://www.youtube.com/watch?v=SdxOouXsaxc 4 min video] of Demis Hassabis and John Jumper reacting to their Nobel Prize.
The [https://www.nobelprize.org/prizes/physics/2024/press-release/ 2024 Nobel Prize in Physics went to John J. Hopfield and Geoffrey E. Hinton] for machine learning with neural networks, technology that underlies the prizewinning work in Chemistry.
</td></tr></table>

In 2020, the '''AlphaFold2'''<ref name="senior202001">PMID: 31942072</ref><ref name="alphafoldwikipedia">[https://en.wikipedia.org/wiki/AlphaFold AlphaFold] at Wikipedia.</ref> system of [https://deepmind.com DeepMind]<ref name="deepmindblog">[https://deepmind.com/blog/article/alphafold-a-solution-to-a-50-year-old-grand-challenge-in-biology AlphaFold: a solution to a 50-year-old grand challenge in biology], DeepMind Blog, November 30, 2020.</ref><ref name="deepmindwikipedia">[https://en.wikipedia.org/wiki/DeepMind DeepMind] at Wikipedia.</ref> demonstrated a '''major breakthrough'''<ref name="alquraishi">[https://moalquraishi.wordpress.com/2020/12/08/alphafold2-casp14-it-feels-like-ones-child-has-left-home/ AlphaFold2 @ CASP14: “It feels like one’s child has left home.”] by Mohammed AlQuraishi, December 8, 2020.</ref><ref name="casppressrelease">[https://predictioncenter.org/casp14/doc/CASP14_press_release.html Artificial intelligence solution to a 50-year-old science challenge could ‘revolutionise’ medical research], CASP Press Release, November 30, 2020.</ref><ref name="callaway" /><ref name="helliwell">[https://www.iucr.org/news/newsletter/volume-28/number-4/deepmind-and-casp14 DeepMind and CASP14] by John R. Helliwell, International Union of Crystallography Newsletter, December 4, 2020.</ref>. At [[Theoretical_models#2020:_CASP_14|CASP14]], AlphaFold2 was far better able, among over 100 competing groups, to '''predict structures, including sidechain positions''', so close to the subsequently revealed X-ray crystallographic structures as to differ by little more than the differences between two independently-determined X-ray structures of the same molecule. It did this for about two-thirds of the targets in the competition. AlphaFold2 has been hailed as '''largely solving the protein structure prediction problem for single-chain proteins'''<ref name="alquraishi" /><ref name="casppressrelease" /><ref name="callaway">PMID: 33257889</ref><ref name="helliwell" />. "Never in my life had I expected to see a scientific advance so rapid." said Mohammed AlQuraishi of Columbia University<ref name="alquraishi" />. But consider also "The joys and perils of AlphaFold"<ref name="perils">PMID: 34668287</ref>.

In 2022, at [[CASP]] 15, AlphaFold2 continued to outperform all other methods in the majority of cases (see a summary of results at [[Theoretical_models#2022:_CASP_15|Theoretical models]]).

In September, 2023, John Jumper and Demis Hassabis received the [https://laskerfoundation.org/winners/alphafold-a-technology-for-predicting-protein-structures Lasker Award] for revolutionizing protein structure prediction<ref name="lasker-scientist">[https://www.the-scientist.com/news/lasker-award-for-revolutionizing-protein-structure-predictions-71386 Lasker Award for Revolutionizing Protein Structure Predictions], Laura Tran, <i>The Scientist</i>, September, 2023.</ref><ref name="lasker-nature">PMID: 37752227</ref>.

<table style="background-color:#e0ffe0;border:1px solid black;font-size:120%;"><tr><td>
If you want an AlphaFold-predicted structure for a protein sequence:
* If a prediction is already in the [[#AlphaFold Database of Predictions|AlphaFold Database]], simply download it. Limited to single chain proteins without ligands.
* Otherwise, and for multiple chain (protein/nucleic acid) structures with ligands, follow [[How to predict structures with AlphaFold]].
* Dropping the predicted model into [http://FirstGlance.Jmol.Org FirstGlance in Jmol] will automatically '''color it by estimated reliability per residue'''. Examples: [http://bioinformatics.org/molvis/images/firstglance-with-alphafold.png Snapshot], [http://firstglance.jmol.org/fg.htm?mol=AF-Q9AY27-F1-model_v1.pdb Interactive].
</td></tr></table>

2021 Resources: [For more recent resources and servers, see [[How to predict structures with AlphaFold]].]
* See [https://www.ebi.ac.uk/training/online/courses/alphafold AlphaFold A practical Guide] Superb EMBL-EBI Interactive online tutorial on AlphaFold2 (~3 hours)
*See short [https://mediasite.embl.de/Mediasite/Play/a320afff218d4a3cbad6ea6eca5212931d superb lecture] on AlphaFold by the CEO of ''DeepMind'', '''Dennis Hassabis''', that was given at the EMBL, Heidelberg, on 3-Feb-2022, entitled '''Using AI to accelerate scientific discovery'''.
*see [https://youtu.be/UqeQfRDA8Yk EMBL-EBI-Training Video] six superb short talks on AlphaFold2
*See [[Theoretical_models#2020:_CASP_14]] for more about the initial success at CASP14, and the reactions to it.
*[[Theoretical_models#AlphaFold2_Methods|AlphaFold2 Methods]]
*[[AlphaFold2_examples_from_CASP_14]] describes a detailed analysis of two of the CASP14 predictions.

==AlphaFold Database of Predictions==

In 2023, the free [https://alphafold.ebi.ac.uk/ AlphaFold Database] has been expanded to >200 million structures. Proteins in
[http://uniprot.org UniProt] now link to the AlphaFold models in the Structure section. For an overview of which proteins are and are not in the AlphaFold Database, see ''Which proteins are included?'' in the FAQ at the main page of AlphaFold Database.

In July, 2021, DeepMind made available over 300,000 structure predictions from amino acid sequences in their free [https://alphafold.ebi.ac.uk/ AlphaFold DB]<ref name="deepminddb">[https://deepmind.com/research/case-studies/alphafold#a_treasure_trove We’ve made AlphaFold predictions freely available to anyone in the scientific community] at DeepMind.com (date of release not specified, approximately July 2021).</ref><ref name="afdbebi">[https://www.ebi.ac.uk/pdbe/about/news/alphafold%E2%80%99s-protein-structure-predictions-now-available-explore AlphaFold’s protein structure predictions now available to explore] at the European Bioinformatics Institute, July 23, 2021.</ref><ref name="impacts">[https://www.embl.org/news/science/alphafold-potential-impacts/ Great expectations – the potential impacts of AlphaFold DB] at the European Bioinformatics Institute, July 22, 2021</ref><ref name="human">[https://www.embl.org/news/science/alphafold-database-launch/ DeepMind and EMBL release the most complete database of predicted 3D structures of human proteins] at the European Bioinformatics Institute, July 22, 2021.</ref>. These predictions include nearly all ~20,000 proteins in the human proteome, 36% with very high confidence, and another 22% with high confidence<ref name="human" /><ref name="human-nature">PMID: 34293799</ref>. Also included are ''E. coli'', fruit fly, mouse, zebrafish, malaria parasite and tuberculosis bacteria<ref name="human" />. Limitations of these predictions were enumerated<ref name="impacts" /><ref name="perils" />, including:
* Inability to predict protein-protein or protein-DNA/RNA/ligand complexes. [[#RoseTTAFold]] and AlphaFold both claim progress on predicting protein-protein complexes.
* Does not predict ligands, cofactors, metals, ions, glycosylation, etc. (Efforts to extend to such: see [[#Ligands: AlphaFill|AlphaFill below]]; and [https://www.nature.com/articles/s41594-021-00680-9 glycolsylations].)
* Does not deal with conformational dynamics.
* Does not predict [[Intrinsically Disordered Protein|intrinsically unstructured]] segments.
* Does not predict the folding pathway.
* Has not been trained to predict structural consequences of '''point mutations'''.

Nevertheless, these predictions have many potential benefits<ref name="impacts" />, including:
* Simplifying [[X-ray crystallography]] by enabling solution of the phase problem by molecular replacement using the predicted model.
* Assisting crystallographers in defining [[domain]] boundaries in order to crystallize domains when crystallization of full length proteins is problematic.
* Helping to interpret >5,000 [[cryo-EM]] maps previously deposited in the [[EMDB]] that could not be interpreted as atomic models, as well as helping to interpret lower resolution EM maps as atomic models.

===Ligands: AlphaFill===
The AlphaFold Database has been enhanced by "transplanting" ligands from empirical structures similar to predicted structures. Results are in the [http://alphafill.eu AlphaFill Database] ([https://biorxiv.org/cgi/content/short/2021.11.26.470110 preprint]). The authors caution
<blockquote>
"AlphaFill models are not meant or suitable for precise quantification of interactions between the transferred ligand(s) and the protein (e.g. hydrogen bonds, π-π or cation-π interactions, van der Waals interactions, hydrophobic interactions, halogen bonds). These require coordinate precision that is not provided by either the AlphaFold or the AlphaFill models at the current stage, and the models should only be interpreted in a qualitative manner."
</blockquote>

==AlphaFold published July 2021==
[For recent prediction servers, see [[How to predict structures with AlphaFold]].]

AlphaFold was published in July, 2021<ref name="af2021">PMID: 34265844</ref>. Methods were described in considerable detail. The source code, trained weights, and inference script were made available under an '''open-source license'''. Structure prediction required about one GPU (Graphics Processing Unit) minute per model of about 384 amino acids.

Impressively, AlphaFold had remarkable success predicting a set of 10,795 protein chain structures (filtered for high reliability, lengths restricted to 80-1,400 residues) published in the [[PDB]] after AlphaFold's training set<ref>The training set cutoff was 2018/04/30. The test set was obtained between then and 2021/02/15.</ref>. Overall alpha carbon accuracy had a median of 1.46 Å [[Calculating GDT TS|RMSD]] at 95% coverage. The majority of chain structures were predicted with full-chain alpha carbon RMSD values <2 Å. About 25% were predicted with RMSD >4 Å.

Importantly, each prediction comes with a confidence score that reliably predicts the accuracy of the predicted structure.

Accurate prediction of sidechains required accurate prediction of the main chain. Accurate prediction required a multiple sequence alignment depth >~30 sequences, with a depth of ~100 sequences being adequate.

==Free AlphaFold-based Servers==

<table style="background-color:#e0ffe0;border:1px solid black;font-size:120%;"><tr><td>
If you want an AlphaFold-predicted structure for a protein sequence:
* If a prediction is already in the [[#AlphaFold Database of Predictions|AlphaFold Database]], simply download it. Limited to single chain proteins without ligands.
* Otherwise, and for multiple chain (protein/nucleic acid) structures with ligands, follow [[How to predict structures with AlphaFold]].
* Uploading the predicted PDB file to [http://FirstGlance.Jmol.Org FirstGlance in Jmol] will automatically '''color it by estimated reliability per residue'''. Examples: [http://bioinformatics.org/molvis/images/firstglance-with-alphafold.png Snapshot], [http://firstglance.jmol.org/fg.htm?mol=AF-Q9AY27-F1-model_v1.pdb Interactive].
</td></tr></table>

===RoseTTAFold===

Also in July, 2021, Minkyung Baek and a large team in the [https://www.bakerlab.org/ group of David Baker] published their '''RoseTTAFold''' employing a three-track network, based in part on methods inspired by AlphaFold but not yet fully-detailed by DeepMind. They reported "accuracies approaching those of DeepMind in CASP14"<ref name="baek1">PMID: 34282049</ref>. At the time of its release in July, 2021, it had outperformed all other available structure prediction ''servers''<ref name="baek1" />.

The [https://robetta.bakerlab.org/ RoseTTAFold Server] was made freely available. (Open the ''Structure Prediction'' menu at the top and choose ''Submit''. At the form, be sure to check ''RoseTTAFold'' before submitting your job).

===AlphaFold Colab===
Google provides "Colaboratories" (Colabs). A Colab "allows anybody to write and execute arbitrary python code through the browser, and is especially well suited to machine learning, data analysis and education"<ref name="colabfaq">[https://research.google.com/colaboratory/faq.html Collaboratory FAQ] at Google.</ref>.

DeepMind has provided an [https://colab.research.google.com/github/deepmind/alphafold/blob/main/notebooks/AlphaFold.ipynb Alphafold Colab] that uses a "slightly simplified" version of AlphaFold version 2.0: "While accuracy will be near-identical to the full AlphaFold system on many targets, a small fraction have a large drop in accuracy due to the smaller MSA and lack of templates.". The AlphaFold Colab is '''free to use'''. The code is executed in a virtual machine private to your account, and data are stored on Google Drive. Nothing is installed on your computer; "everything happens in the cloud on Google Colab"<ref name="alphafoldcolab">[https://colab.research.google.com/github/deepmind/alphafold/blob/main/notebooks/AlphaFold.ipynb Alphafold Colab].</ref> See [[How to predict structures with AlphaFold]].

For those unfamiliar with Colabs, the user interface may look unfamiliar, but the instructions are clear and straightforward to use. The mentions of "Runtime -> Run after" refer to the Runtime pull-down menu at the very top of the page. Getting a result may take several hours.

===ColabFold: AlphaFold2 with MMSeqs2===

[https://colab.research.google.com/github/sokrypton/ColabFold/blob/main/AlphaFold2.ipynb A colab by Sergey Ovchinnikov, Milot Mirdita and Martin Steinegger]. In their [https://www.biorxiv.org/content/10.1101/2021.08.15.456425v1 accompanying publication] they state:
<blockquote>
"MMseqs2’s MSAs [multiple sequence alignments] produce more accurate predictions while being ~16 faster compared to the AlphaFold2’s MSA stage. ColabFold also offers many advanced features, such as homo- and hetero-complex modeling and exposes AlphaFold2 internals."
</blockquote>

===Current offerings via Colab===

Work is ongoing and other offerings are now available on Colab for RoseTTAFold and AlphaFold2 besides the ones detailed above. This summary guide & video should help in choosing how to analyze your proteins of interest:

- [https://github.com/sokrypton/ColabFold#making-protein-folding-accessible-to-all-via-google-colab A Guide to the free RoseTTAFold and AlphaFold 2 Colab notebooks]

- ColabFold: A [https://www.youtube.com/watch?v=Rfw7thgGTwI video covering an overview, comparison of some of the methods and how people are already extending them, how to submit and interpret, and a tutorial on how to use AlphaFold2 Colab] is available. The video was recorded on August 4th, 2021 presented by Sergey Ovchinnikov and Martin Steinegger, hosted by Chris Bahl for the Boston Protein Design and Modeling Club

==Advances since 2021==
*See a list of newer servers at [[How to predict structures with AlphaFold]].
*RoseTTAFoldNA<ref>PMID: 37996753</ref> offers a leap forward in predicting structures of complexes of proteins and nucleic acids, but in November 2023 is not yet available as a free server.

==See Also==
*[[How to predict structures with AlphaFold]].
*[[AlphaFold/Index]], a list of pages in Proteopedia about Alphafold.
*[[How To Find A Structure]] covers both [[empirical models]] and the advantages of comparing them with AlphaFold models due to [[missing residues and incomplete sidechains]] prevalent in empirical models.

==References==
<references />

==Further reading==

* '''AlphaFold protein structure predictions - a step change for biology.'''
: (Report by Oana Stroe, Senior Communications Officer at EMBL-EBI. 28 July 2021 at [https://bit.ly/2UZREPx FEBS Network])
: Sameer Velankar and Gerard Kleywegt, from the Protein Data Bank in Europe, and Alex Bateman, Head of Protein Sequence Resources, all at EMBL’s European Bioinformatics Institute (EMBL-EBI), explore the research avenues opened up by the AlphaFold database and explain the method's limitations.

* '''A structural biology community assessment of AlphaFold 2 applications.'''
: Akdel et al., 2021
: https://biorxiv.org/cgi/content/short/2021.09.26.461876
: Several findings:
:: AlphaFold 2 can often predict the correct homo-oligomer structure when given the correct oligomeric state (number of copies in complex); however, it's not always able to predict the correct oligomeric state ''a priori''.
:: "AF2 models can be used across diverse applications equally well compared to experimentally determined structures, when the confidence metrics are critically considered."

* '''Protein complex prediction with AlphaFold-Multimer '''
: Evans et al., 2021
: https://www.biorxiv.org/content/10.1101/2021.10.04.463034
: Highlights:
:: Fine tuned Alphafold 2 model for protein interaction predictions.
:: "The source code and weights for the trained models will be made available shortly."

User talk:Xuguang Jiang

2026-09-19T15:34:01Z

Eric Martz: Welcome!

User:Xuguang Jiang

2026-09-19T15:34:01Z

Eric Martz: Creating user page for new user.

Position: JSPS international postdoctoral fellow
Institution (NO ABBREVIATIONS): The University of Tokyo
City: Bunkyo
State/Province: Tokyo
Country: Japan
Field of Expertise or Study: Biochemistry; Cell biology
ORCID ID: https://orcid.org/0000-0001-7997-872X

User talk:Caroline Castro Hawrylyszyn

2026-09-19T15:32:07Z

Eric Martz: Welcome!

User:Caroline Castro Hawrylyszyn

2026-09-19T15:32:07Z

Eric Martz: Creating user page for new user.

Position: Estudante
Institution (NO ABBREVIATIONS): Universidade do Minho
City: Braga
State/Province: Braga
Country: Portugal
Field of Expertise or Study: Bioquímica

FirstGlance in Jmol Literature Citations

2026-08-24T16:47:19Z

Eric Martz:

The following publications in the scientific literature cite use of ''[[FirstGlance in Jmol]]''. This list excludes publications co-authored by [[User:Eric Martz]], the author of ''FirstGlance in Jmol''. (Those are listed at [https://scholar.google.com/citations?user=Bb3H0OsAAAAJ&hl=en&oi=ao Google Scholar: Eric Martz].) The >120 citations listed below in more than 30 [[#Journals Cited|peer-reviewed journals]] were found by searching full text using [https://scholar.google.com Google Scholar] (see [[#Coverage|Coverage]]), and all were verified to cite ''FirstGlance in Jmol''.
<table align="right" class="wikitable" width="500"><tr><td>
[[FirstGlance in Jmol]] offers, since 2006, free visualization and analysis of protein molecules and other macromolecules (DNA, RNA, oligosaccharides, etc.). It is easy to use and provides built-in guidance and help. In 2024, it was used on average '''265 times/day'''. For more, see
* [[FirstGlance in Jmol]]
* [http://firstglance.jmol.org/whatis.htm#unique Unique Capabilities of FirstGlance in Jmol]
* [https://www.youtube.com/@ericmartz9100 FirstGlance YouTube Channel] [[Image:Youtube.png]]
* [[FirstGlance/Index]], a list of resources about FirstGlance in Jmol, including all the relevant pages in Proteopedia.
* [http://firstglance.jmol.org Start FirstGlance in Jmol]
</td></tr></table>
Researchers took advantage of [http://firstglance.jmol.org/whatis.htm#unique unique capabilities] of ''FirstGlance'':
<ul>
<li>Visual analysis of structures predicted by '''AlphaFold2''', colored by '''reliability''' estimates.
<li>Calculation of average '''pLDDT''' for structures predicted by '''AlphaFold3'''.
<li>Seeing locations of [[Missing residues and incomplete sidechains|'''missing''' residues]], which affect shape, distribution of polar/hydrophobic surfaces, and may result in missing [[salt bridges]] and [[cation-pi interactions]].
<li>Locating '''mutations''' in the 3D model.
<li>Positions of proteins in lipid bilayer '''membranes''' (models from [https://opm.phar.umich.edu/ OPM U. Mich.]).
<li>Coloring amino acids by evolutionary '''conservation''' (determined by [https://consurf.tau.ac.il ConSurf]) to identify functional sites.
<li>Rejection of models with '''Rfree''' below average for their resolutions.
<li>Applying sequence '''numbering''' to the 3D view.
<li>Seeing the distribution of hydrophobic vs. '''polar''' amino acids.
<li>Percentages of '''secondary''' structure elements.
<li>Locating residues or regions of interest, using ''Find'' to apply yellow '''halos'''.
<li>Distribution and counts of '''charged''' residues.
<li>Visual '''isolation''' of domains or regions of interest.
<li>Identification of '''contact residues'''.
</ul>
<span style="background-color:#fffce0;">Use your browser's ''Find in page'' (Control-f / Command-f) to locate studies involving the '''bold''' terms above. Some of these capabilities are illustrated with animations generated by ''FirstGlance'' at [https://tinyurl.com/movingmolecules tinyurl.com/movingmolecules].</span>
__NOTOC__

==2026==

==={{Font color|#ff8000|Education & Communication}}===

<ref group="xtra">PMID: 41854287</ref><references group="xtra" />

==={{Font color|#00b000|BioMedical Research}}===

<ref group="xtra">PMID: 42527684</ref><references group="xtra" />

<ref group="xtra">PMID: 42375539</ref><references group="xtra" />

<ref group="xtra">PMID: 42395897</ref><references group="xtra" />

<ref group="xtra">PMID: 42344113</ref><references group="xtra" />

<ref group="xtra">PMID: 41504448</ref><references group="xtra" />

==2021-2025==

==={{Font color|#ff8000|Education & Communication}}===

<ref group="xtra">PMID: 39976303</ref><references group="xtra" />

* [https://www.google.com/books/edition/Food_Chemistry_in_Small_Bites/QLk_EQAAQBAJ O'Hara, Patricia B. Food Chemistry in Small Bites: The Alchemist in the Kitchen. Univ of California Press; 2025 Apr 15.]

<ref group="xtra">PMID: 39291955</ref><references group="xtra" />

<ref group="xtra">PMID: 35001912</ref><references group="xtra" />

==={{Font color|#00b000|BioMedical Research}}===
====2025====
<ref group="xtra">PMID: 41390121</ref><references group="xtra" />

<ref group="xtra">PMID: 41060696</ref><references group="xtra" />
<blockquote><span style="background-color:#fffce0;">
For AlphaFold3-predicted structures, "Average '''pLDDT''' scores were calculated using FirstGlance in Jmol."
</span>
</blockquote>

<ref group="xtra">PMID: 41331102</ref><references group="xtra" />

<ref group="xtra">PMID: 41047069</ref><references group="xtra" />

<ref group="xtra">PMID: 41072766</ref><references group="xtra" />

<table align="right"><tr><td>
[[Image:Sefid-consurf-teplizumab-2025.png]]
</td><td width="250">
Figure 2 from Sefid ''et al.'', 2025.
'''Conservation''' of amino acids in Teplizumab analyzed using the ConSurf Server and displayed by FirstGlance in Jmol.
Reproduced in accord with the Creative Commons Attribution Deed<ref name="cca4i" />
</td></tr></table>
* [https://d1wqtxts1xzle7.cloudfront.net/123175184/4_DR_sefid-libre.pdf Sefid F, Monshizadeh K, Ghenaatzadeh R, Roodgarpour Z, Azamirad G, Mirhosseini H. Antibody Engineering Toward Enhancement of Teplizumab Anti-CD3 Binding Affinity in Type 1 Diabetes Prevention and Treatment. Iranian Journal of Diabetes and Obesity. 2025 May 10;17(2):97-109.]

<table align="right"><tr><td>
[[Image:Garcia-e-lyta-fig5-microorgs2025.png|300px]]
</td><td width="250">
Figure 5 from García, 2025. Molecular rendering of [[4x36]] by FirstGlance in Jmol. Reproduced with written permission from Ernesto Garcia (April 29, 2025).
</td></tr></table>
<ref group="xtra">PMID: 40284663</ref><references group="xtra" />

<ref group="xtra">PMID: 39299531</ref><references group="xtra" />

* [https://www.biorxiv.org/content/10.1101/2025.04.11.648320v1.full Weber H, Ehinger A, Kolb D, Fallahzadeh-Mamaghani V, Halter T, Franz-Wachtel M, zur Oven-Krockhaus S, Gronnier J, Zipfel C, Harter K, Kemmerling B. Arabidopsis HYPERSENSITIVE INDUCED REACTION 2 affects plasma membrane receptor pathways and organization. bioRxiv. 2025:2025-04.]
<blockquote>
<span style="background-color:#fffce0;">"AlphaFold2 modeling of HIR2 and analysis of the '''distribution of polar amino acids by FirstGlance''' revealed an N-terminal surface-exposed platform of HIR2 that consists of nonpolar residues, which could interact with hydrophobic parts of the (plasma) membrane."</span>
</blockquote>

<ref group="xtra">PMID: 39758030</ref><references group="xtra" />

====2024====
<table align="right"><tr><td>
[[Image:Martinez-alcantar-2024-fig1-1ol5.png|500px]]
</td><td width="250">
Fig. 1, [[1ol5]], from Martinez ''et al.'', 2024. Molecular rendering and Å scale by FirstGlance in Jmol; black labels added by Martinez ''et al.''.
Reproduced in accord with the Creative Commons Attribution Deed<ref name="cca4i">This work was published under the [https://creativecommons.org/licenses/by/4.0/ Creative Commons Attribution 4.0 International Deed].</ref>.
</td></tr></table>

<ref group="xtra">PMID: 39636801</ref><references group="xtra" />
<blockquote>
<span style="background-color:#fffce0;">FirstGlance in Jmol was used to visualize and tabulate '''missing residues''' in [[2az5]].</span>
(See [[Missing residues and incomplete sidechains]].)
</blockquote>

* [https://publish.kne-publishing.com/index.php/IJDO/article/view/15710 Sefid, Fateme, et al. "Antibody Engineering to Enhancement of Ranibizumab Binding Affinity for the Prevention and Treatment of Diabetic Retinopathy." Iranian journal of diabetes and obesity (2024).]

<ref group="xtra">PMID: 37904054</ref><references group="xtra" />

* [https://www.mdpi.com/2813-3757/2/4/23 Martínez-Alcantar, Lorena, et al. "Cyclic Peptides as Protein Kinase Modulators and Their Involvement in the Treatment of Diverse Human Diseases." Kinases and Phosphatases 2.4 (2024): 346-378.]

<ref group="xtra">PMID: 38968704</ref><references group="xtra" />
<blockquote>
<span style="background-color:#fffce0;">FirstGlance was used to visualize models predicted by '''AlphaFold2, colored by reliablity scores'''.</span>
</blockquote>

<table align="right"><tr><td>
[[Image:Gajta et al 2024 Fig3C Isolated domain from AlphaFold2.png|400px]]
</td><td width="250">
Fig. 3C, and AlphaFold2 prediction, from Gajda ''et al.'', 2024. Isolation of this domain, sequence numbering (applied with a single checkbox), and molecular rendering by FirstGlance in Jmol.
Reproduced in accord with the Creative Commons Attribution Deed<ref name="cca4i" />.
</td></tr></table>

<ref group="xtra">PMID: 38731903</ref><references group="xtra" />

<ref group="xtra">PMID: 39052973</ref><references group="xtra" />
<blockquote>
<span style="background-color:#fffce0;">'''Transmembrane secondary structure segments''' were evaluated using FirstGlance prior to docking analysis.</span>
</blockquote>

* [https://onlinelibrary.wiley.com/doi/full/10.1155/2024/1575103 Pan Y, Yao X, Yang TN, Li JL, Shi DF. The VP1/2 Protein of a New Recombinant PRV Strain Promotes the Infectivity and Pathogenicity of PRV in Northeastern China. Transboundary and Emerging Diseases. 2024;2024(1):1575103.]
<blockquote>
<span style="background-color:#fffce0;">FirstGlance was used to '''locate mutations''' in the 3D structure.</span>
</blockquote>

====2023====

<ref group="xtra">PMID: 37154976</ref><references group="xtra" />

<ref group="xtra">PMID: 37464933</ref><references group="xtra" />

* [https://www.biorxiv.org/content/10.1101/2023.05.28.542320.abstract Sondhi Y, Messcher RL, Bellantuano AJ, Storer CG, Cinel SD, Godfrey RK, Glass D, St Laurent RA, Hamilton CA, Earl C, Brislawn CJ. The developmental gene disco regulates diel-niche evolution in adult moths. bioRxiv. 2023 May 28:2023-05.]

* [https://dc.etsu.edu/context/etd/article/5760/viewcontent/PremaA052323f.pdf Prema A. Mapping The Binding Site Within Integrin αD β2 for Carboxyethylpyrrole (CEP)-Modified Proteins (2023). Electronic Theses and Dissertations, East Tennessee State University. Paper 4232.]

* [https://link.springer.com/article/10.1007/s11816-022-00788-4 Hassan MM, Martin S, Feng K, Yates TB, Yuan G, Martin MZ, Martin S, Muchero W, Griffiths NA, Weston DJ, Yang X. Genome-wide identification and functional prediction of silicon (Si) transporters in poplar (Populus trichocarpa). Plant Biotechnology Reports. 2023 Apr;17(2):285-302.]

<ref group="xtra">PMID: 36670408</ref><references group="xtra" />

====2022====
<table align="right"><tr><td>
[[Image:Puccio-2021-mol-micro.png|300px]]
</td><td width="250">
Graphical Abstract from Puccio ''et al.'', 2022. Molecular rendering by FirstGlance in Jmol. <font color="red">'''Red'''</font> and <font color="blue">'''Blue'''</font> planes represent boundaries of the lipid bilayer membrane. Reproduced in accord with the Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International
Deed<ref name="ccannd4i">This work was published under the [https://creativecommons.org/licenses/by-nc-nd/4.0/ Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International Deed].</ref>.
</td></tr></table>
<ref group="xtra">PMID: 34855265</ref><references group="xtra" />
<blockquote>
<span style="background-color:#fffce0;">"'''Positions within a cellular membrane''' were predicted using OPM (https://opm.phar.umich.edu/) and visualized in JMol 3.0 using FirstGlance."</span>
</blockquote>

<ref group="xtra">PMID: 35869579</ref><references group="xtra" />

<ref group="xtra">PMID: 36120551</ref><references group="xtra" />

<ref group="xtra">PMID: 35537348</ref><references group="xtra" />

<table align="right"><tr><td>
[[Image:Camelo, lopez-pazos 2022 fig 7-CClic.png|400px]]
</td><td width="250">
Figure 5 from Camelo ''et al.'', 2025. Molecular rendering by FirstGlance in Jmol. Reproduced in accord with the Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International
Deed<ref name="ccansa4i">This work was published under the [https://creativecommons.org/licenses/by-nc-sa/4.0/deed.en Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International Deed].</ref>.
</td></tr></table>
* [http://scielo.senescyt.gob.ec/scielo.php?pid=S1390-85962022000200032&script=sci_abstract&tlng=en Lozano Camelo OC, Rojas Arias AC, Ávila Méndez KJ, López-Pazos SA. Preservación modificada y descripción de la fungalisina para Batrachochytrium dendrobatidis. LA GRANJA. Revista de Ciencias de la Vida. 2022 Feb;36(2):32-44.]

<ref group="xtra">PMID: 35493110</ref><references group="xtra" />

<ref group="xtra">PMID: 35742992</ref><references group="xtra" />

* [https://dl.acm.org/doi/abs/10.1145/3570773.3570833 Xu Y. The Analysis of Tiotropium bromide and Roflumilast: Two Potent Medications for Chronic Obstructive Pulmonary Disease. InProceedings of the 3rd International Symposium on Artificial Intelligence for Medicine Sciences 2022 Oct 13 (pp. 231-238).]

<ref group="xtra">PMID: 35228627</ref><references group="xtra" />

<ref group="xtra">PMID: 35139120</ref><references group="xtra" />

====2021====

<ref group="xtra">PMID: 34619810</ref><references group="xtra" />

<ref group="xtra">PMID: 32496928</ref><references group="xtra" />

<ref group="xtra">PMID: 34786595</ref><references group="xtra" />

* [https://www.frontiersin.org/articles/10.3389/fevo.2021.666564/full Junker N, Gossmann TI. Adaptation-driven evolution of sirtuin 1 (SIRT1), a key regulator of metabolism and aging, in marmot species. Frontiers in Ecology and Evolution. 2021 Jul 2;9:666564.]

* [http://jommid.pasteur.ac.ir/browse.php?a_id=345&sid=1&slc_lang=en&ftxt=0 Sefid F, Khalesi B, Mansoori B, Fotovvat M, Touhidinia M. Enhancement of SARS-CoV-2 Receptor Binding Domain-CR3022 Human Antibody Binding Affinity via In silico Engineering Approach. Journal of Medical Microbiology and Infectious Diseases. 2021 Sep 10;9(3):156-69.]

* [https://link.springer.com/article/10.1007/s10725-021-00735-3 Brunoni F, Rolli E, Polverini E, Spíchal L, Ricci A. The adjuvant activity of two urea derivatives on cytokinins: An example of serendipitous dual effect. Plant Growth Regulation. 2021 Nov;95:169-90.]

==2016-2020==

==={{Font color|#ff8000|Education & Communication}}===

<ref group="xtra">PMID: 32077575</ref><references group="xtra" />
<blockquote>
<span style="background-color:#fffce0;">Lee ''et al.'', 2020, said "... browser-based applications or interfaces (e.g., ''FirstGlance in Jmol'') increase accessibility for students. Hands-on use of visualization software by students seems to benefit their 3D understanding of proteins better than simply viewing it on-screen."</span>
</blockquote>

* [https://pubs.acs.org/doi/10.1021/acs.jchemed.8b00426 Cation−Π Interactions in Biochemistry: A Primer, Miguel O. Mitchell and John Means, J. Chem. Educ. 2018, 95, 12, 2284–2288.]

<ref group="xtra">PMID: 28214437</ref><references group="xtra" />

==={{Font color|#00b000|BioMedical Research}}===
====2020====
<table align="right"><tr><td>
[[Image:Lin et al 2020 Fig2d 1hk0.png|300px]]
</td><td width="250">
Fig. 2d from Lin ''et al.'', 2020. '''Secondary structure percentages''' and molecular rendering by ''FirstGlance in Jmol''.
Reproduced in accord with the Creative Commons Attribution-NonCommercial 4.0 International
Deed<ref name="ccanc4i">This work was published under the [https://creativecommons.org/licenses/by-nc/4.0/ Creative Commons Attribution-NonCommercial 4.0 International Deed].</ref>.
</td></tr></table>
<ref group="xtra">PMID: 33460241</ref><references group="xtra" />

<ref group="xtra">PMID: 31702846</ref><references group="xtra" />
<blockquote>
<span style="background-color:#fffce0;">Ben Chorin ''et al.'', 2020, wrote "The '''conservation grades (colors) are mapped onto the three-dimensional structure of the query protein''', which can be viewed using ... FirstGlance in Jmol. This visualization is highly enlightening because it emphasizes the important, evolutionarily conserved regions of the protein."</span>
</blockquote>

<ref group="xtra">PMID: 31608807</ref><references group="xtra" />

<table align="right"><tr><td>
[[Image:McGurk et la 2020 Fig 2I,J tankyrase-binding domain halos 4bs2.png|500px]]
</td><td width="250">
Portions of Fig. 2I,J from McGurk ''et al.'', 2020. The '''tankyrase-binding-domain of [[4bs2]] was identified ({{Yelspan|yellow halos}}) with the ''Find'' tool''' of ''FirstGlance in Jmol''. ''FirstGlance'' also added the sequence labels.
Reproduced in accord with the Creative Commons Attribution 4.0 International
Deed<ref name="cca4i" />.
</td></tr></table>
<ref group="xtra">PMID: 32409565</ref><references group="xtra" />

<ref group="xtra">PMID: 32531564</ref><references group="xtra" />

<ref group="xtra">PMID: 32706779</ref><references group="xtra" />
<blockquote>
<span style="background-color:#fffce0;">Shalit and Tuvi-Arad, 2020, wrote "For each protein [565 were analyzed], we calculated the Rfree grade as defined by FirstGlance in Jmol .... '''Files were kept if their Rfree grade was at least "average" at their resolution.'''"</span>
</blockquote>

<ref group="xtra">PMID: 32123543</ref><references group="xtra" />
<blockquote>
<span style="background-color:#fffce0;">Mattila ''et al.'' 2020 provided a downloadable PDB file with a link to view it by uploading to ''FirstGlance in Jmol''.</span>
</blockquote>

<ref group="xtra">PMID: 32867961</ref><references group="xtra" />

* [http://op.niscpr.res.in/index.php/IJBB/article/viewFile/29116/465477657 Zaheer ZA, Sankaranarayanan K. In silico analysis of κ-theraphotoxin-Cg2a from Chilobrachys guangxiensis. Indian Journal of Biochemistry and Biophysics (IJBB). 2020 Jul 28;57(4):458-66.]

====2019====
<ref group="xtra">PMID: 31058389</ref><references group="xtra" />

<ref group="xtra">PMID: 31172379</ref><references group="xtra" />

<ref group="xtra">PMID: 31018129</ref><references group="xtra" />

<ref group="xtra">PMID: 30791384</ref><references group="xtra" />

====2018====
<ref group="xtra">PMID: 30346734</ref><references group="xtra" />

<ref group="xtra">PMID: 29534001</ref><references group="xtra" />

<ref group="xtra">PMID: 29567208</ref><references group="xtra" />

<ref group="xtra">PMID: 30398106</ref><references group="xtra" />

<ref group="xtra">PMID: 29684709</ref><references group="xtra" />

<ref group="xtra">PMID: 29704154</ref><references group="xtra" />

<ref group="xtra">PMID: 30381731</ref><references group="xtra" />

* [https://link.springer.com/article/10.1134/S1068162018020024 Podlesnykh SV, Shanshin DV, Kolosova EA, Murashkin DE, Shaprova ON, Shcherbakov DN, Chapoval AI. Development of Search Strategy for Peptide Inhibitors of Immune Checkpoints. Russian Journal of Bioorganic Chemistry. 2018 Mar;44:150-7.]

====2017====

<ref group="xtra">PMID: 29262419</ref><references group="xtra" />

<ref group="xtra">PMID: 28791129</ref><references group="xtra" />

<ref group="xtra">PMID: 29079705</ref><references group="xtra" />

<ref group="xtra">PMID: 28302399</ref><references group="xtra" />

<ref group="xtra">PMID: 28872841</ref><references group="xtra" />

<ref group="xtra">PMID: 28434129</ref><references group="xtra" />

<ref group="xtra">PMID: 30258911</ref><references group="xtra" />

====2016====

* [https://www.researchgate.net/profile/Rahul-Shelake/publication/309241483_Structural_Analysis_and_Homology_Modeling_of_Members_of_smt-like_Operon_from_Thermophilic_Cyanobacterium_Thermosynechococcus_elongatus_BP-1/links/58099b9708ae1c98c25263e3/Structural-Analysis-and-Homology-Modeling-of-Members-of-smt-like-Operon-from-Thermophilic-Cyanobacterium-Thermosynechococcus-elongatus-BP-1.pdf Shelake RM, Hayashi H, Morita EH. Structural analysis and homology modeling of members of smt-like operon from thermophilic cyanobacterium Thermosynechococcus elongatus BP-1. J Proteins Proteomics. 2016;7(3):221-30.]

<ref group="xtra">PMID: 27400707</ref><references group="xtra" />

<ref group="xtra">PMID: 26866676</ref><references group="xtra" />
<blockquote>
<span style="background-color:#fffce0;">See Figure 2 which uses ''FirstGlance in Jmol'' to '''highlight critical lysine residues''' in nucleosome histones with yellow halos. That Figure is not reproduced here because ACS denies permission to non-profit organizations, unless payment is made.</span>
</blockquote>

<ref group="xtra">PMID: 26043781</ref><references group="xtra" />
<blockquote>
<span style="background-color:#fffce0;">''FirstGlance in Jmol'' was used to '''locate and count charged residues'''.</span>
</blockquote>

<ref group="xtra">PMID: 27347491</ref><references group="xtra" />

* [https://www.academia.edu/download/79451787/medicinalchemistry-2-1016.pdf Santiago-Ruiz S, Polverini E, Manjarrez J, Espinoza KA, Reynoso E, Rivero IA. Virtual Screening of Putative Anticonvulsant Hydantoin Derived Drugs and Biological Evaluation. Ann. Med. Chem. Res. 2016;2(1):1016-23.]

<ref group="xtra">PMID: 26608339</ref><references group="xtra" />

==2011-2015==

===Coverage===
<table style="background-color:#ffe0e0;"><tr><td>
Coverage is nearly complete for the most recent decade 2016-2025 (above), as far as publications found with the methods used<ref name="gsmethods">In scholar.google.com, the query ''firstglance'' finds mostly irrelevant papers with the term ''first glance''. Quoting the query, ''"firstglance"'' was used to restrict hits to that exact single word. However, some papers erroneously cite ''First Glance in Jmol'', or even say something like ''Jmol, with the First Glance''. Therefore, a second search was done using ''"first glance" and jmol''.</ref> in [https://scholar.google.com Google Scholar]. For years before 2016 (below), only an arbitrary subset of citations is listed.
</td></tr></table>

==={{Font color|#ff8000|Education & Communication}}===

<ref group="xtra">PMID: 24591499</ref><references group="xtra" />
<blockquote>
<span style="background-color:#fffce0;">Barber & Stark wrote "FirstGlance in Jmol is a simple platform with sophisticated functionality for viewing a molecule's structure with different diagrams, cross-sections, and emphasis on various molecular features."</span>
</blockquote>

<ref group="xtra">PMID: 24979189</ref><references group="xtra" />

<ref group="xtra">PMID: 23649886</ref><references group="xtra" />

* [https://onlinelibrary.wiley.com/doi/abs/10.1002/ijch.201300024 Hanson RM, Prilusky J, Renjian Z, Nakane T, Sussman JL. JSmol and the next‐generation web‐based representation of 3D molecular structure as applied to proteopedia. Israel Journal of Chemistry. 2013 Apr;53(3‐4):207-16.]

<ref group="xtra">PMID: 23354749</ref><references group="xtra" />
<blockquote>
<span style="background-color:#fffce0;">Forest writes "Structures should be made to come alive in articles. ... [A] straightforward option is to include a link to the NSF-supported Java-based application ''Firstglance in Jmol'' that will allow the reader to call up the pdb file in a simple Web-based viewer that is browser independent."</span>
</blockquote>

<ref group="xtra">PMID: 24019219</ref><references group="xtra" />
<blockquote>
<span style="background-color:#fffce0;">Figure 1 is an excellent example of how a student used ''FirstGlance in Jmol'' to '''visualize hydrophobic cores'''. That Figure is not reproduced here because obtaining permission from Wiley Publications is complicated and may require payment even for a non-profit educational organization with open access on the Internet.</span>
</blockquote>

<ref group="xtra">PMID: 23166023</ref><references group="xtra" />
<blockquote>
<span style="background-color:#fffce0;">''FirstGlance in Jmol'' was the sole 3D visualization tool provided to students in this study.</span>
</blockquote>

* [https://pubs.acs.org/doi/full/10.1021/ed101022g Saderholm, Matthew, and Anthony Reynolds. "Jmol-enhanced biochemistry research projects." Journal of Chemical Education 88.8 (2011): 1074-1078.].

==={{Font color|#00b000|BioMedical Research}}===
<span style="background-color:#ffe0e0;">[[#Coverage|Partial Coverage]]</span>

<ref group="xtra">PMID: 25785714</ref><references group="xtra" />

<ref group="xtra">PMID: 26224535</ref><references group="xtra" />

<table align="right"><tr><td>
[[Image:Chen et al 2012 Fig 1 3g04.png|500px]]
</td><td width="250">
Fig. 1 from Chen ''et al.'', 2012. Atomic rendering of the leucine-rich repeat domain of the thyroid-stimulating hormone receptor by ''FirstGlance in Jmol'' showing hydrophobic vs. polar regions and charge distribution.
Yellow halos highlight charged residues at the C-terminal "base" of the domain.
Reproduced in accord with the Creative Commons Attribution 4.0 International
Deed<ref name="cca4i" />.
</td></tr></table>

<ref group="xtra">PMID: 25336027</ref><references group="xtra" />

<ref group="xtra">PMID: 24692644</ref><references group="xtra" />

* [https://pubs.acs.org/doi/abs/10.1021/bk-2013-1142.ch016 Fleming SA. Teaching tools for organic and bio-organic chemistry. In Pedagogic Roles of Animations and Simulations in Chemistry Courses 2013 (pp. 389-409). American Chemical Society.]

<ref group="xtra">PMID: 22359649</ref><references group="xtra" />

<ref group="xtra">PMID: 22235356</ref><references group="xtra" />

<ref group="xtra">PMID: 23119066</ref><references group="xtra" />

<ref group="xtra">PMID: 22069494</ref><references group="xtra" />

<ref group="xtra">PMID: 21472436</ref><references group="xtra" />
<blockquote>
<span style="background-color:#fffce0;">In 2011, the '''Protein Structure Initiative's''' Structural Biology '''Knowledgebase''' offers ''FirstGlance in Jmol'' as a structure viewer.</span>
</blockquote>

<ref group="xtra">PMID: 22440564</ref><references group="xtra" />

==2006-2010==

==={{Font color|#ff8000|Education & Communication}}===
<span style="background-color:#ffe0e0;">[[#Coverage|Partial Coverage]]</span>

<ref group="xtra">PMID: 21567875</ref><references group="xtra" />
<blockquote>
<span style="background-color:#fffce0;">... applications such as the excellent, FirstGlance in Jmol provide a quick and simple way to view and manipulate structures ....</span>
</blockquote>

<ref group="xtra">PMID: 20504857</ref><references group="xtra" />
<blockquote>
<span style="background-color:#fffce0;">Porollo and Meller wrote "Protein–ligand contacts are determined using the respective procedure adopted in Protein Explorer and subsequently in the FirstGlance in Jmol server (FGiJ) that accounts for hydrogen bonds, water and salt bridges, hydrophobic and aromatic ring interaction and different types of metals binding. For the corresponding bond distance definitions, the reader is referred to the FGiJ documentation." '''This excellent server continues to be available in 2025''' as [https://polyview.cchmc.org/polyview3d.html PolyView-3D], and is linked at the Martz website [http://molviz.org MolviZ.Org].</span>
</blockquote>

<ref group="xtra">PMID: 20541422</ref><references group="xtra" />

<ref group="xtra">PMID: 20195256</ref><references group="xtra" />

<ref group="xtra">PMID: 21567685</ref><references group="xtra" />
<blockquote>
<span style="background-color:#fffce0;">''FirstGlance in Jmol'' was the primary visualization package provided to students in this curriculum.</span>
</blockquote>

<ref group="xtra">PMID: 19230677</ref><references group="xtra" />
<blockquote>
<span style="background-color:#fffce0;">Hodis and Sussman wrote "... widely available
molecular visualization programs ... are
often inaccessible to non-specialists owing to a steep learning curve (with, in our opinion, FirstGlance in Jmol being an exception)."</span>
</blockquote>

<ref group="xtra">PMID: 19847312</ref><references group="xtra" />

* [https://pmc.ncbi.nlm.nih.gov/articles/PMC2762578/ Palmer III AG, Matthews BW. Interactive graphics return to protein science. Protein Science: A Publication of the Protein Society. 2009 Mar 20;18(4):677.]

<ref group="xtra">PMID: 19461848</ref><references group="xtra" />
<blockquote>
<span style="background-color:#fffce0;">Interactivity allows a reader unbounded scope to explore a structure, taking advantage of whatever features the visualization software may provide. This is the basis underlying FirstGlance in Jmol, a service that an increasing number of journals link to, which provides standard buttons to view different aspects of a protein structure ....</span>
</blockquote>

<ref group="xtra">PMID: 21638687</ref><references group="xtra" />
<blockquote>
<span style="background-color:#fffce0;">Herráez said "I express my gratitude to Prof. Eric Martz (University of Massachusetts), long-time advocate of molecular modeling teaching, provider of Rasmol and Chime information and support on his website, of teaching-oriented recommendations and sample materials, of the excellent Protein Explorer software for macromolecule visualization and analysis, and of other countless contributions, including the recent FirstGlance in Jmol."</span>
</blockquote>

==={{Font color|#00b000|BioMedical Research}}===
<span style="background-color:#ffe0e0;">[[#Coverage|Partial Coverage]]</span>

<ref group="xtra">PMID: 20634950</ref><references group="xtra" />
<blockquote>
<span style="background-color:#fffce0;">''FirstGlance in Jmol'' was used to visualize patterns of '''evolutionary conservation''' calculated by the [http://consurf.tau.ac.il ConSurf Server].</span>
</blockquote>

<ref group="xtra">PMID: 21029378</ref><references group="xtra" />

<ref group="xtra">PMID: 18971256</ref><references group="xtra" />

<ref group="xtra">PMID: 19329630</ref><references group="xtra" />

<ref group="xtra">PMID: 19233205</ref><references group="xtra" />

* [https://books.google.com/books?hl=en&lr=&id=3jq1kSKcvEAC&oi=fnd&pg=PR11&dq=firstglance&ots=XchA-jpK7C&sig=TKhk00SK4YHR3QtLqXZU23d0jK8 Courey AJ. Mechanisms in transcriptional regulation. John Wiley & Sons; 2009 Jan 22.]
<blockquote>
<span style="background-color:#fffce0;">"''FirstGlance in Jmol'': This free program, also developed by Eric Martz, is probably '''the easiest way to look at macromolecules'''."</span>
</blockquote>

<ref group="xtra">PMID: 18067320</ref><references group="xtra" />
<blockquote>
<span style="background-color:#fffce0;">"The "'''contact residues'''" of the SH3 domain with the ligand were assigned by means of the FirstGlance in Jmol program ...."</span>
</blockquote>

<ref group="xtra">PMID: 19081051</ref><references group="xtra" />

<ref group="xtra">PMID: 18347046</ref><references group="xtra" />

==Journals Cited==

Peer-reviewed scientific papers listed above that cite ''FirstGlance in Jmol'' were published in numerous journals, including
===Education Journals===
''Biochemistry and Molecular Biology Education (8), Journal of Chemical Education.''

===Basic Research Journals===
''ACS Chemical Biology, Archives of Biophysics & Biochemistry, Biochemistry (3), BMC Microbiology, Cell Reports, Current Opinion in Virology, European Journal of Cell Biology, FEBS Journal, Gene, Journal of Cell Science, Journal of Bacteriology (2), Journal of Biological Chemistry, Journal of Molecular Biology, Molecular Microbiology, Nature Methods, Nucleic Acids Research (2), Planta, Plant Growth Regulation, Plant Cell Reports, PLOS One (9), Protein Science (3), Structure*, Scientific Reports, Trends in Biochemical Sciences (2), Veterinary Journal''.

<nowiki>*</nowiki> Nimrod ''et al.'', 2008.

===Medical Journals===
''Annals of Neurology, Infection & Immunity, Leukemia, Medical Microbiology & Immunology, PLOS Neglected Tropical Diseases.''

==References==
<references />

FirstGlance in Jmol Literature Citations

2026-08-23T21:30:20Z

Eric Martz: /* 2026 */

The following publications in the scientific literature cite use of ''[[FirstGlance in Jmol]]''. This list excludes publications co-authored by [[User:Eric Martz]], the author of ''FirstGlance in Jmol''. (Those are listed at [https://scholar.google.com/citations?user=Bb3H0OsAAAAJ&hl=en&oi=ao Google Scholar: Eric Martz].) The 120 citations listed below in more than 30 [[#Journals Cited|peer-reviewed journals]] were found by searching full text using [https://scholar.google.com Google Scholar] (see [[#Coverage|Coverage]]), and all were verified to cite ''FirstGlance in Jmol''.
<table align="right" class="wikitable" width="500"><tr><td>
[[FirstGlance in Jmol]] offers, since 2006, free visualization and analysis of protein molecules and other macromolecules (DNA, RNA, oligosaccharides, etc.). It is easy to use and provides built-in guidance and help. In 2024, it was used on average '''265 times/day'''. For more, see
* [[FirstGlance in Jmol]]
* [http://firstglance.jmol.org/whatis.htm#unique Unique Capabilities of FirstGlance in Jmol]
* [https://www.youtube.com/@ericmartz9100 FirstGlance YouTube Channel] [[Image:Youtube.png]]
* [[FirstGlance/Index]], a list of resources about FirstGlance in Jmol, including all the relevant pages in Proteopedia.
* [http://firstglance.jmol.org Start FirstGlance in Jmol]
</td></tr></table>
Researchers took advantage of [http://firstglance.jmol.org/whatis.htm#unique unique capabilities] of ''FirstGlance'':
<ul>
<li>Visual analysis of structures predicted by '''AlphaFold2''', colored by '''reliability''' estimates.
<li>Calculation of average '''pLDDT''' for structures predicted by '''AlphaFold3'''.
<li>Seeing locations of [[Missing residues and incomplete sidechains|'''missing''' residues]], which affect shape, distribution of polar/hydrophobic surfaces, and may result in missing [[salt bridges]] and [[cation-pi interactions]].
<li>Locating '''mutations''' in the 3D model.
<li>Positions of proteins in lipid bilayer '''membranes''' (models from [https://opm.phar.umich.edu/ OPM U. Mich.]).
<li>Coloring amino acids by evolutionary '''conservation''' (determined by [https://consurf.tau.ac.il ConSurf]) to identify functional sites.
<li>Rejection of models with '''Rfree''' below average for their resolutions.
<li>Applying sequence '''numbering''' to the 3D view.
<li>Seeing the distribution of hydrophobic vs. '''polar''' amino acids.
<li>Percentages of '''secondary''' structure elements.
<li>Locating residues or regions of interest, using ''Find'' to apply yellow '''halos'''.
<li>Distribution and counts of '''charged''' residues.
<li>Visual '''isolation''' of domains or regions of interest.
<li>Identification of '''contact residues'''.
</ul>
<span style="background-color:#fffce0;">Use your browser's ''Find in page'' (Control-f / Command-f) to locate studies involving the '''bold''' terms above. Some of these capabilities are illustrated with animations generated by ''FirstGlance'' at [https://tinyurl.com/movingmolecules tinyurl.com/movingmolecules].</span>
__NOTOC__

==2026==

==={{Font color|#ff8000|Education & Communication}}===

<ref group="xtra">PMID: 41854287</ref><references group="xtra" />

==={{Font color|#00b000|BioMedical Research}}===

<ref group="xtra">PMID: 42527684</ref><references group="xtra" />

<ref group="xtra">PMID: 42375539</ref><references group="xtra" />

<ref group="xtra">PMID: 42395897</ref><references group="xtra" />

<ref group="xtra">PMID: 42344113</ref><references group="xtra" />

<ref group="xtra">PMID: 41504448</ref><references group="xtra" />

==2021-2025==

==={{Font color|#ff8000|Education & Communication}}===

<ref group="xtra">PMID: 39976303</ref><references group="xtra" />

* [https://www.google.com/books/edition/Food_Chemistry_in_Small_Bites/QLk_EQAAQBAJ O'Hara, Patricia B. Food Chemistry in Small Bites: The Alchemist in the Kitchen. Univ of California Press; 2025 Apr 15.]

<ref group="xtra">PMID: 39291955</ref><references group="xtra" />

<ref group="xtra">PMID: 35001912</ref><references group="xtra" />

==={{Font color|#00b000|BioMedical Research}}===
====2025====
<ref group="xtra">PMID: 41390121</ref><references group="xtra" />

<ref group="xtra">PMID: 41060696</ref><references group="xtra" />
<blockquote><span style="background-color:#fffce0;">
For AlphaFold3-predicted structures, "Average '''pLDDT''' scores were calculated using FirstGlance in Jmol."
</span>
</blockquote>

<ref group="xtra">PMID: 41331102</ref><references group="xtra" />

<ref group="xtra">PMID: 41047069</ref><references group="xtra" />

<ref group="xtra">PMID: 41072766</ref><references group="xtra" />

<table align="right"><tr><td>
[[Image:Sefid-consurf-teplizumab-2025.png]]
</td><td width="250">
Figure 2 from Sefid ''et al.'', 2025.
'''Conservation''' of amino acids in Teplizumab analyzed using the ConSurf Server and displayed by FirstGlance in Jmol.
Reproduced in accord with the Creative Commons Attribution Deed<ref name="cca4i" />
</td></tr></table>
* [https://d1wqtxts1xzle7.cloudfront.net/123175184/4_DR_sefid-libre.pdf Sefid F, Monshizadeh K, Ghenaatzadeh R, Roodgarpour Z, Azamirad G, Mirhosseini H. Antibody Engineering Toward Enhancement of Teplizumab Anti-CD3 Binding Affinity in Type 1 Diabetes Prevention and Treatment. Iranian Journal of Diabetes and Obesity. 2025 May 10;17(2):97-109.]

<table align="right"><tr><td>
[[Image:Garcia-e-lyta-fig5-microorgs2025.png|300px]]
</td><td width="250">
Figure 5 from García, 2025. Molecular rendering of [[4x36]] by FirstGlance in Jmol. Reproduced with written permission from Ernesto Garcia (April 29, 2025).
</td></tr></table>
<ref group="xtra">PMID: 40284663</ref><references group="xtra" />

<ref group="xtra">PMID: 39299531</ref><references group="xtra" />

* [https://www.biorxiv.org/content/10.1101/2025.04.11.648320v1.full Weber H, Ehinger A, Kolb D, Fallahzadeh-Mamaghani V, Halter T, Franz-Wachtel M, zur Oven-Krockhaus S, Gronnier J, Zipfel C, Harter K, Kemmerling B. Arabidopsis HYPERSENSITIVE INDUCED REACTION 2 affects plasma membrane receptor pathways and organization. bioRxiv. 2025:2025-04.]
<blockquote>
<span style="background-color:#fffce0;">"AlphaFold2 modeling of HIR2 and analysis of the '''distribution of polar amino acids by FirstGlance''' revealed an N-terminal surface-exposed platform of HIR2 that consists of nonpolar residues, which could interact with hydrophobic parts of the (plasma) membrane."</span>
</blockquote>

<ref group="xtra">PMID: 39758030</ref><references group="xtra" />

====2024====
<table align="right"><tr><td>
[[Image:Martinez-alcantar-2024-fig1-1ol5.png|500px]]
</td><td width="250">
Fig. 1, [[1ol5]], from Martinez ''et al.'', 2024. Molecular rendering and Å scale by FirstGlance in Jmol; black labels added by Martinez ''et al.''.
Reproduced in accord with the Creative Commons Attribution Deed<ref name="cca4i">This work was published under the [https://creativecommons.org/licenses/by/4.0/ Creative Commons Attribution 4.0 International Deed].</ref>.
</td></tr></table>

<ref group="xtra">PMID: 39636801</ref><references group="xtra" />
<blockquote>
<span style="background-color:#fffce0;">FirstGlance in Jmol was used to visualize and tabulate '''missing residues''' in [[2az5]].</span>
(See [[Missing residues and incomplete sidechains]].)
</blockquote>

* [https://publish.kne-publishing.com/index.php/IJDO/article/view/15710 Sefid, Fateme, et al. "Antibody Engineering to Enhancement of Ranibizumab Binding Affinity for the Prevention and Treatment of Diabetic Retinopathy." Iranian journal of diabetes and obesity (2024).]

<ref group="xtra">PMID: 37904054</ref><references group="xtra" />

* [https://www.mdpi.com/2813-3757/2/4/23 Martínez-Alcantar, Lorena, et al. "Cyclic Peptides as Protein Kinase Modulators and Their Involvement in the Treatment of Diverse Human Diseases." Kinases and Phosphatases 2.4 (2024): 346-378.]

<ref group="xtra">PMID: 38968704</ref><references group="xtra" />
<blockquote>
<span style="background-color:#fffce0;">FirstGlance was used to visualize models predicted by '''AlphaFold2, colored by reliablity scores'''.</span>
</blockquote>

<table align="right"><tr><td>
[[Image:Gajta et al 2024 Fig3C Isolated domain from AlphaFold2.png|400px]]
</td><td width="250">
Fig. 3C, and AlphaFold2 prediction, from Gajda ''et al.'', 2024. Isolation of this domain, sequence numbering (applied with a single checkbox), and molecular rendering by FirstGlance in Jmol.
Reproduced in accord with the Creative Commons Attribution Deed<ref name="cca4i" />.
</td></tr></table>

<ref group="xtra">PMID: 38731903</ref><references group="xtra" />

<ref group="xtra">PMID: 39052973</ref><references group="xtra" />
<blockquote>
<span style="background-color:#fffce0;">'''Transmembrane secondary structure segments''' were evaluated using FirstGlance prior to docking analysis.</span>
</blockquote>

* [https://onlinelibrary.wiley.com/doi/full/10.1155/2024/1575103 Pan Y, Yao X, Yang TN, Li JL, Shi DF. The VP1/2 Protein of a New Recombinant PRV Strain Promotes the Infectivity and Pathogenicity of PRV in Northeastern China. Transboundary and Emerging Diseases. 2024;2024(1):1575103.]
<blockquote>
<span style="background-color:#fffce0;">FirstGlance was used to '''locate mutations''' in the 3D structure.</span>
</blockquote>

====2023====

<ref group="xtra">PMID: 37154976</ref><references group="xtra" />

<ref group="xtra">PMID: 37464933</ref><references group="xtra" />

* [https://www.biorxiv.org/content/10.1101/2023.05.28.542320.abstract Sondhi Y, Messcher RL, Bellantuano AJ, Storer CG, Cinel SD, Godfrey RK, Glass D, St Laurent RA, Hamilton CA, Earl C, Brislawn CJ. The developmental gene disco regulates diel-niche evolution in adult moths. bioRxiv. 2023 May 28:2023-05.]

* [https://dc.etsu.edu/context/etd/article/5760/viewcontent/PremaA052323f.pdf Prema A. Mapping The Binding Site Within Integrin αD β2 for Carboxyethylpyrrole (CEP)-Modified Proteins (2023). Electronic Theses and Dissertations, East Tennessee State University. Paper 4232.]

* [https://link.springer.com/article/10.1007/s11816-022-00788-4 Hassan MM, Martin S, Feng K, Yates TB, Yuan G, Martin MZ, Martin S, Muchero W, Griffiths NA, Weston DJ, Yang X. Genome-wide identification and functional prediction of silicon (Si) transporters in poplar (Populus trichocarpa). Plant Biotechnology Reports. 2023 Apr;17(2):285-302.]

<ref group="xtra">PMID: 36670408</ref><references group="xtra" />

====2022====
<table align="right"><tr><td>
[[Image:Puccio-2021-mol-micro.png|300px]]
</td><td width="250">
Graphical Abstract from Puccio ''et al.'', 2022. Molecular rendering by FirstGlance in Jmol. <font color="red">'''Red'''</font> and <font color="blue">'''Blue'''</font> planes represent boundaries of the lipid bilayer membrane. Reproduced in accord with the Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International
Deed<ref name="ccannd4i">This work was published under the [https://creativecommons.org/licenses/by-nc-nd/4.0/ Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International Deed].</ref>.
</td></tr></table>
<ref group="xtra">PMID: 34855265</ref><references group="xtra" />
<blockquote>
<span style="background-color:#fffce0;">"'''Positions within a cellular membrane''' were predicted using OPM (https://opm.phar.umich.edu/) and visualized in JMol 3.0 using FirstGlance."</span>
</blockquote>

<ref group="xtra">PMID: 35869579</ref><references group="xtra" />

<ref group="xtra">PMID: 36120551</ref><references group="xtra" />

<ref group="xtra">PMID: 35537348</ref><references group="xtra" />

<table align="right"><tr><td>
[[Image:Camelo, lopez-pazos 2022 fig 7-CClic.png|400px]]
</td><td width="250">
Figure 5 from Camelo ''et al.'', 2025. Molecular rendering by FirstGlance in Jmol. Reproduced in accord with the Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International
Deed<ref name="ccansa4i">This work was published under the [https://creativecommons.org/licenses/by-nc-sa/4.0/deed.en Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International Deed].</ref>.
</td></tr></table>
* [http://scielo.senescyt.gob.ec/scielo.php?pid=S1390-85962022000200032&script=sci_abstract&tlng=en Lozano Camelo OC, Rojas Arias AC, Ávila Méndez KJ, López-Pazos SA. Preservación modificada y descripción de la fungalisina para Batrachochytrium dendrobatidis. LA GRANJA. Revista de Ciencias de la Vida. 2022 Feb;36(2):32-44.]

<ref group="xtra">PMID: 35493110</ref><references group="xtra" />

<ref group="xtra">PMID: 35742992</ref><references group="xtra" />

* [https://dl.acm.org/doi/abs/10.1145/3570773.3570833 Xu Y. The Analysis of Tiotropium bromide and Roflumilast: Two Potent Medications for Chronic Obstructive Pulmonary Disease. InProceedings of the 3rd International Symposium on Artificial Intelligence for Medicine Sciences 2022 Oct 13 (pp. 231-238).]

<ref group="xtra">PMID: 35228627</ref><references group="xtra" />

<ref group="xtra">PMID: 35139120</ref><references group="xtra" />

====2021====

<ref group="xtra">PMID: 34619810</ref><references group="xtra" />

<ref group="xtra">PMID: 32496928</ref><references group="xtra" />

<ref group="xtra">PMID: 34786595</ref><references group="xtra" />

* [https://www.frontiersin.org/articles/10.3389/fevo.2021.666564/full Junker N, Gossmann TI. Adaptation-driven evolution of sirtuin 1 (SIRT1), a key regulator of metabolism and aging, in marmot species. Frontiers in Ecology and Evolution. 2021 Jul 2;9:666564.]

* [http://jommid.pasteur.ac.ir/browse.php?a_id=345&sid=1&slc_lang=en&ftxt=0 Sefid F, Khalesi B, Mansoori B, Fotovvat M, Touhidinia M. Enhancement of SARS-CoV-2 Receptor Binding Domain-CR3022 Human Antibody Binding Affinity via In silico Engineering Approach. Journal of Medical Microbiology and Infectious Diseases. 2021 Sep 10;9(3):156-69.]

* [https://link.springer.com/article/10.1007/s10725-021-00735-3 Brunoni F, Rolli E, Polverini E, Spíchal L, Ricci A. The adjuvant activity of two urea derivatives on cytokinins: An example of serendipitous dual effect. Plant Growth Regulation. 2021 Nov;95:169-90.]

==2016-2020==

==={{Font color|#ff8000|Education & Communication}}===

<ref group="xtra">PMID: 32077575</ref><references group="xtra" />
<blockquote>
<span style="background-color:#fffce0;">Lee ''et al.'', 2020, said "... browser-based applications or interfaces (e.g., ''FirstGlance in Jmol'') increase accessibility for students. Hands-on use of visualization software by students seems to benefit their 3D understanding of proteins better than simply viewing it on-screen."</span>
</blockquote>

* [https://pubs.acs.org/doi/10.1021/acs.jchemed.8b00426 Cation−Π Interactions in Biochemistry: A Primer, Miguel O. Mitchell and John Means, J. Chem. Educ. 2018, 95, 12, 2284–2288.]

<ref group="xtra">PMID: 28214437</ref><references group="xtra" />

==={{Font color|#00b000|BioMedical Research}}===
====2020====
<table align="right"><tr><td>
[[Image:Lin et al 2020 Fig2d 1hk0.png|300px]]
</td><td width="250">
Fig. 2d from Lin ''et al.'', 2020. '''Secondary structure percentages''' and molecular rendering by ''FirstGlance in Jmol''.
Reproduced in accord with the Creative Commons Attribution-NonCommercial 4.0 International
Deed<ref name="ccanc4i">This work was published under the [https://creativecommons.org/licenses/by-nc/4.0/ Creative Commons Attribution-NonCommercial 4.0 International Deed].</ref>.
</td></tr></table>
<ref group="xtra">PMID: 33460241</ref><references group="xtra" />

<ref group="xtra">PMID: 31702846</ref><references group="xtra" />
<blockquote>
<span style="background-color:#fffce0;">Ben Chorin ''et al.'', 2020, wrote "The '''conservation grades (colors) are mapped onto the three-dimensional structure of the query protein''', which can be viewed using ... FirstGlance in Jmol. This visualization is highly enlightening because it emphasizes the important, evolutionarily conserved regions of the protein."</span>
</blockquote>

<ref group="xtra">PMID: 31608807</ref><references group="xtra" />

<table align="right"><tr><td>
[[Image:McGurk et la 2020 Fig 2I,J tankyrase-binding domain halos 4bs2.png|500px]]
</td><td width="250">
Portions of Fig. 2I,J from McGurk ''et al.'', 2020. The '''tankyrase-binding-domain of [[4bs2]] was identified ({{Yelspan|yellow halos}}) with the ''Find'' tool''' of ''FirstGlance in Jmol''. ''FirstGlance'' also added the sequence labels.
Reproduced in accord with the Creative Commons Attribution 4.0 International
Deed<ref name="cca4i" />.
</td></tr></table>
<ref group="xtra">PMID: 32409565</ref><references group="xtra" />

<ref group="xtra">PMID: 32531564</ref><references group="xtra" />

<ref group="xtra">PMID: 32706779</ref><references group="xtra" />
<blockquote>
<span style="background-color:#fffce0;">Shalit and Tuvi-Arad, 2020, wrote "For each protein [565 were analyzed], we calculated the Rfree grade as defined by FirstGlance in Jmol .... '''Files were kept if their Rfree grade was at least "average" at their resolution.'''"</span>
</blockquote>

<ref group="xtra">PMID: 32123543</ref><references group="xtra" />
<blockquote>
<span style="background-color:#fffce0;">Mattila ''et al.'' 2020 provided a downloadable PDB file with a link to view it by uploading to ''FirstGlance in Jmol''.</span>
</blockquote>

<ref group="xtra">PMID: 32867961</ref><references group="xtra" />

* [http://op.niscpr.res.in/index.php/IJBB/article/viewFile/29116/465477657 Zaheer ZA, Sankaranarayanan K. In silico analysis of κ-theraphotoxin-Cg2a from Chilobrachys guangxiensis. Indian Journal of Biochemistry and Biophysics (IJBB). 2020 Jul 28;57(4):458-66.]

====2019====
<ref group="xtra">PMID: 31058389</ref><references group="xtra" />

<ref group="xtra">PMID: 31172379</ref><references group="xtra" />

<ref group="xtra">PMID: 31018129</ref><references group="xtra" />

<ref group="xtra">PMID: 30791384</ref><references group="xtra" />

====2018====
<ref group="xtra">PMID: 30346734</ref><references group="xtra" />

<ref group="xtra">PMID: 29534001</ref><references group="xtra" />

<ref group="xtra">PMID: 29567208</ref><references group="xtra" />

<ref group="xtra">PMID: 30398106</ref><references group="xtra" />

<ref group="xtra">PMID: 29684709</ref><references group="xtra" />

<ref group="xtra">PMID: 29704154</ref><references group="xtra" />

<ref group="xtra">PMID: 30381731</ref><references group="xtra" />

* [https://link.springer.com/article/10.1134/S1068162018020024 Podlesnykh SV, Shanshin DV, Kolosova EA, Murashkin DE, Shaprova ON, Shcherbakov DN, Chapoval AI. Development of Search Strategy for Peptide Inhibitors of Immune Checkpoints. Russian Journal of Bioorganic Chemistry. 2018 Mar;44:150-7.]

====2017====

<ref group="xtra">PMID: 29262419</ref><references group="xtra" />

<ref group="xtra">PMID: 28791129</ref><references group="xtra" />

<ref group="xtra">PMID: 29079705</ref><references group="xtra" />

<ref group="xtra">PMID: 28302399</ref><references group="xtra" />

<ref group="xtra">PMID: 28872841</ref><references group="xtra" />

<ref group="xtra">PMID: 28434129</ref><references group="xtra" />

<ref group="xtra">PMID: 30258911</ref><references group="xtra" />

====2016====

* [https://www.researchgate.net/profile/Rahul-Shelake/publication/309241483_Structural_Analysis_and_Homology_Modeling_of_Members_of_smt-like_Operon_from_Thermophilic_Cyanobacterium_Thermosynechococcus_elongatus_BP-1/links/58099b9708ae1c98c25263e3/Structural-Analysis-and-Homology-Modeling-of-Members-of-smt-like-Operon-from-Thermophilic-Cyanobacterium-Thermosynechococcus-elongatus-BP-1.pdf Shelake RM, Hayashi H, Morita EH. Structural analysis and homology modeling of members of smt-like operon from thermophilic cyanobacterium Thermosynechococcus elongatus BP-1. J Proteins Proteomics. 2016;7(3):221-30.]

<ref group="xtra">PMID: 27400707</ref><references group="xtra" />

<ref group="xtra">PMID: 26866676</ref><references group="xtra" />
<blockquote>
<span style="background-color:#fffce0;">See Figure 2 which uses ''FirstGlance in Jmol'' to '''highlight critical lysine residues''' in nucleosome histones with yellow halos. That Figure is not reproduced here because ACS denies permission to non-profit organizations, unless payment is made.</span>
</blockquote>

<ref group="xtra">PMID: 26043781</ref><references group="xtra" />
<blockquote>
<span style="background-color:#fffce0;">''FirstGlance in Jmol'' was used to '''locate and count charged residues'''.</span>
</blockquote>

<ref group="xtra">PMID: 27347491</ref><references group="xtra" />

* [https://www.academia.edu/download/79451787/medicinalchemistry-2-1016.pdf Santiago-Ruiz S, Polverini E, Manjarrez J, Espinoza KA, Reynoso E, Rivero IA. Virtual Screening of Putative Anticonvulsant Hydantoin Derived Drugs and Biological Evaluation. Ann. Med. Chem. Res. 2016;2(1):1016-23.]

<ref group="xtra">PMID: 26608339</ref><references group="xtra" />

==2011-2015==

===Coverage===
<table style="background-color:#ffe0e0;"><tr><td>
Coverage is nearly complete for the most recent decade 2016-2025 (above), as far as publications found with the methods used<ref name="gsmethods">In scholar.google.com, the query ''firstglance'' finds mostly irrelevant papers with the term ''first glance''. Quoting the query, ''"firstglance"'' was used to restrict hits to that exact single word. However, some papers erroneously cite ''First Glance in Jmol'', or even say something like ''Jmol, with the First Glance''. Therefore, a second search was done using ''"first glance" and jmol''.</ref> in [https://scholar.google.com Google Scholar]. For years before 2016 (below), only an arbitrary subset of citations is listed.
</td></tr></table>

==={{Font color|#ff8000|Education & Communication}}===

<ref group="xtra">PMID: 24591499</ref><references group="xtra" />
<blockquote>
<span style="background-color:#fffce0;">Barber & Stark wrote "FirstGlance in Jmol is a simple platform with sophisticated functionality for viewing a molecule's structure with different diagrams, cross-sections, and emphasis on various molecular features."</span>
</blockquote>

<ref group="xtra">PMID: 24979189</ref><references group="xtra" />

<ref group="xtra">PMID: 23649886</ref><references group="xtra" />

* [https://onlinelibrary.wiley.com/doi/abs/10.1002/ijch.201300024 Hanson RM, Prilusky J, Renjian Z, Nakane T, Sussman JL. JSmol and the next‐generation web‐based representation of 3D molecular structure as applied to proteopedia. Israel Journal of Chemistry. 2013 Apr;53(3‐4):207-16.]

<ref group="xtra">PMID: 23354749</ref><references group="xtra" />
<blockquote>
<span style="background-color:#fffce0;">Forest writes "Structures should be made to come alive in articles. ... [A] straightforward option is to include a link to the NSF-supported Java-based application ''Firstglance in Jmol'' that will allow the reader to call up the pdb file in a simple Web-based viewer that is browser independent."</span>
</blockquote>

<ref group="xtra">PMID: 24019219</ref><references group="xtra" />
<blockquote>
<span style="background-color:#fffce0;">Figure 1 is an excellent example of how a student used ''FirstGlance in Jmol'' to '''visualize hydrophobic cores'''. That Figure is not reproduced here because obtaining permission from Wiley Publications is complicated and may require payment even for a non-profit educational organization with open access on the Internet.</span>
</blockquote>

<ref group="xtra">PMID: 23166023</ref><references group="xtra" />
<blockquote>
<span style="background-color:#fffce0;">''FirstGlance in Jmol'' was the sole 3D visualization tool provided to students in this study.</span>
</blockquote>

* [https://pubs.acs.org/doi/full/10.1021/ed101022g Saderholm, Matthew, and Anthony Reynolds. "Jmol-enhanced biochemistry research projects." Journal of Chemical Education 88.8 (2011): 1074-1078.].

==={{Font color|#00b000|BioMedical Research}}===
<span style="background-color:#ffe0e0;">[[#Coverage|Partial Coverage]]</span>

<ref group="xtra">PMID: 25785714</ref><references group="xtra" />

<ref group="xtra">PMID: 26224535</ref><references group="xtra" />

<table align="right"><tr><td>
[[Image:Chen et al 2012 Fig 1 3g04.png|500px]]
</td><td width="250">
Fig. 1 from Chen ''et al.'', 2012. Atomic rendering of the leucine-rich repeat domain of the thyroid-stimulating hormone receptor by ''FirstGlance in Jmol'' showing hydrophobic vs. polar regions and charge distribution.
Yellow halos highlight charged residues at the C-terminal "base" of the domain.
Reproduced in accord with the Creative Commons Attribution 4.0 International
Deed<ref name="cca4i" />.
</td></tr></table>

<ref group="xtra">PMID: 25336027</ref><references group="xtra" />

<ref group="xtra">PMID: 24692644</ref><references group="xtra" />

* [https://pubs.acs.org/doi/abs/10.1021/bk-2013-1142.ch016 Fleming SA. Teaching tools for organic and bio-organic chemistry. In Pedagogic Roles of Animations and Simulations in Chemistry Courses 2013 (pp. 389-409). American Chemical Society.]

<ref group="xtra">PMID: 22359649</ref><references group="xtra" />

<ref group="xtra">PMID: 22235356</ref><references group="xtra" />

<ref group="xtra">PMID: 23119066</ref><references group="xtra" />

<ref group="xtra">PMID: 22069494</ref><references group="xtra" />

<ref group="xtra">PMID: 21472436</ref><references group="xtra" />
<blockquote>
<span style="background-color:#fffce0;">In 2011, the '''Protein Structure Initiative's''' Structural Biology '''Knowledgebase''' offers ''FirstGlance in Jmol'' as a structure viewer.</span>
</blockquote>

<ref group="xtra">PMID: 22440564</ref><references group="xtra" />

==2006-2010==

==={{Font color|#ff8000|Education & Communication}}===
<span style="background-color:#ffe0e0;">[[#Coverage|Partial Coverage]]</span>

<ref group="xtra">PMID: 21567875</ref><references group="xtra" />
<blockquote>
<span style="background-color:#fffce0;">... applications such as the excellent, FirstGlance in Jmol provide a quick and simple way to view and manipulate structures ....</span>
</blockquote>

<ref group="xtra">PMID: 20504857</ref><references group="xtra" />
<blockquote>
<span style="background-color:#fffce0;">Porollo and Meller wrote "Protein–ligand contacts are determined using the respective procedure adopted in Protein Explorer and subsequently in the FirstGlance in Jmol server (FGiJ) that accounts for hydrogen bonds, water and salt bridges, hydrophobic and aromatic ring interaction and different types of metals binding. For the corresponding bond distance definitions, the reader is referred to the FGiJ documentation." '''This excellent server continues to be available in 2025''' as [https://polyview.cchmc.org/polyview3d.html PolyView-3D], and is linked at the Martz website [http://molviz.org MolviZ.Org].</span>
</blockquote>

<ref group="xtra">PMID: 20541422</ref><references group="xtra" />

<ref group="xtra">PMID: 20195256</ref><references group="xtra" />

<ref group="xtra">PMID: 21567685</ref><references group="xtra" />
<blockquote>
<span style="background-color:#fffce0;">''FirstGlance in Jmol'' was the primary visualization package provided to students in this curriculum.</span>
</blockquote>

<ref group="xtra">PMID: 19230677</ref><references group="xtra" />
<blockquote>
<span style="background-color:#fffce0;">Hodis and Sussman wrote "... widely available
molecular visualization programs ... are
often inaccessible to non-specialists owing to a steep learning curve (with, in our opinion, FirstGlance in Jmol being an exception)."</span>
</blockquote>

<ref group="xtra">PMID: 19847312</ref><references group="xtra" />

* [https://pmc.ncbi.nlm.nih.gov/articles/PMC2762578/ Palmer III AG, Matthews BW. Interactive graphics return to protein science. Protein Science: A Publication of the Protein Society. 2009 Mar 20;18(4):677.]

<ref group="xtra">PMID: 19461848</ref><references group="xtra" />
<blockquote>
<span style="background-color:#fffce0;">Interactivity allows a reader unbounded scope to explore a structure, taking advantage of whatever features the visualization software may provide. This is the basis underlying FirstGlance in Jmol, a service that an increasing number of journals link to, which provides standard buttons to view different aspects of a protein structure ....</span>
</blockquote>

<ref group="xtra">PMID: 21638687</ref><references group="xtra" />
<blockquote>
<span style="background-color:#fffce0;">Herráez said "I express my gratitude to Prof. Eric Martz (University of Massachusetts), long-time advocate of molecular modeling teaching, provider of Rasmol and Chime information and support on his website, of teaching-oriented recommendations and sample materials, of the excellent Protein Explorer software for macromolecule visualization and analysis, and of other countless contributions, including the recent FirstGlance in Jmol."</span>
</blockquote>

==={{Font color|#00b000|BioMedical Research}}===
<span style="background-color:#ffe0e0;">[[#Coverage|Partial Coverage]]</span>

<ref group="xtra">PMID: 20634950</ref><references group="xtra" />
<blockquote>
<span style="background-color:#fffce0;">''FirstGlance in Jmol'' was used to visualize patterns of '''evolutionary conservation''' calculated by the [http://consurf.tau.ac.il ConSurf Server].</span>
</blockquote>

<ref group="xtra">PMID: 21029378</ref><references group="xtra" />

<ref group="xtra">PMID: 18971256</ref><references group="xtra" />

<ref group="xtra">PMID: 19329630</ref><references group="xtra" />

<ref group="xtra">PMID: 19233205</ref><references group="xtra" />

* [https://books.google.com/books?hl=en&lr=&id=3jq1kSKcvEAC&oi=fnd&pg=PR11&dq=firstglance&ots=XchA-jpK7C&sig=TKhk00SK4YHR3QtLqXZU23d0jK8 Courey AJ. Mechanisms in transcriptional regulation. John Wiley & Sons; 2009 Jan 22.]
<blockquote>
<span style="background-color:#fffce0;">"''FirstGlance in Jmol'': This free program, also developed by Eric Martz, is probably '''the easiest way to look at macromolecules'''."</span>
</blockquote>

<ref group="xtra">PMID: 18067320</ref><references group="xtra" />
<blockquote>
<span style="background-color:#fffce0;">"The "'''contact residues'''" of the SH3 domain with the ligand were assigned by means of the FirstGlance in Jmol program ...."</span>
</blockquote>

<ref group="xtra">PMID: 19081051</ref><references group="xtra" />

<ref group="xtra">PMID: 18347046</ref><references group="xtra" />

==Journals Cited==

Peer-reviewed scientific papers listed above that cite ''FirstGlance in Jmol'' were published in numerous journals, including
===Education Journals===
''Biochemistry and Molecular Biology Education (8), Journal of Chemical Education.''

===Basic Research Journals===
''ACS Chemical Biology, Archives of Biophysics & Biochemistry, Biochemistry (3), BMC Microbiology, Cell Reports, Current Opinion in Virology, European Journal of Cell Biology, FEBS Journal, Gene, Journal of Cell Science, Journal of Bacteriology (2), Journal of Biological Chemistry, Journal of Molecular Biology, Molecular Microbiology, Nature Methods, Nucleic Acids Research (2), Planta, Plant Growth Regulation, Plant Cell Reports, PLOS One (9), Protein Science (3), Structure*, Scientific Reports, Trends in Biochemical Sciences (2), Veterinary Journal''.

<nowiki>*</nowiki> Nimrod ''et al.'', 2008.

===Medical Journals===
''Annals of Neurology, Infection & Immunity, Leukemia, Medical Microbiology & Immunology, PLOS Neglected Tropical Diseases.''

==References==
<references />

User:Eric Martz/Sandbox 20

2026-08-21T19:10:58Z

Eric Martz:

<StructureSection load='' size='350' side='right' caption='' scene=''>

* <scene name='10/1034703/One/1'>Scene One</scene> of [[3RCB]]

This scene was saved with the automatic color key legend NOT checked, but the key displays anyway:
* <scene name='10/1034703/One/2'>Scene One with NO HALOS when saved (halos on, but no atoms selected)</scene>

</StructureSection>
== References ==
<references/>

User:Eric Martz/Sandbox 20

2026-08-21T19:10:45Z

Eric Martz:

User:Eric Martz/Sandbox 20

2026-08-21T17:40:57Z

Eric Martz:

<StructureSection load='' size='350' side='right' caption='' scene=''>

* <scene name='10/1034703/One/1'>Scene One</scene> of [[3RCB]]
* <scene name='10/1034703/One/2'>Scene One with NO HALOS when saved (halos on, but no atoms selected)</scene>

</StructureSection>
== References ==
<references/>

User:Eric Martz/Sandbox 20

2026-08-21T17:27:51Z

Eric Martz:

<StructureSection load='' size='350' side='right' caption='' scene=''>

* <scene name='10/1034703/One/1'>Scene One</scene> of [[3RCB]]

</StructureSection>
== References ==
<references/>

User:Eric Martz/Sandbox 20

2026-08-21T16:59:25Z

Eric Martz:

<StructureSection load='' size='350' side='right' caption='' scene=''>

</StructureSection>
== References ==
<references/>

Converting AlphaFold3 CIF to PDB

2026-08-18T18:30:43Z

Eric Martz:

The [https://alphafoldserver.com AlphaFold3 Server] predicts models only in the [[Mmcif format|mmCIF format]] (filename ending '''.cif'''). These files<ref name="best">Each job produces 5 .cif files. The file with a name ending   _model_0.cif is one of those with the highest overall [https://alphafoldserver.com/faq pTM quality score]. The pTM quality score is in the corresponding '''_summary_confidences_0.json''' file. Open this file in a [[Help:Plain text editors|text editor]]. Look for the third-from-last line, which begins "ptm": (including the quotes) followed by the overall pTM confidence value. See the FAQ at the [https://alphafoldserver.com AlphaFold3 Server] for how to interpret pTM.</ref> can be visualized & analyzed using ''FirstGlance in Jmol '''version 4.6''''' (or later) available via '''[http://firstglance.jmol.org firstglance.jmol.org]'''. These mmCIF files can also be uploaded to [[iCn3D]], or displayed in [[PyMOL]] or [[ChimeraX]].

Only [http://firstglance.jmol.org FirstGlance in Jmol] and [[iCn3D]] automatically color AlphaFold-predicted models by confidence/[[pLDDT]] correctly ('''{{Font color|blue|blue for high confidence}}, {{Font color|red|red for low confidence}}'''). See [[How_to_predict_structures_with_AlphaFold#Visualizing_Predicted_Structures|Visualizing Predicted Structures]].

FirstGlance also makes it [[FirstGlance/How to get average pLDDT from AlphaFold models|easy to get the average pLDDT]] for any range of residues that you specify.

The original version of this article discussed a method for converting AlphaFold 3 .cif models to .pdb format. ''''That is no longer necessary.'''' ''FirstGlance in Jmol '''version 4.6''''' accepts AlphaFold 3 .cif files directly via drag and drop.

About 5% of the models in the [[wwPDB]] are available only in mmCIF format ("CIF-only"). These are more complicated than AlphaFold models, and are not yet supported by FirstGlance. Support is expected later in 2026.

==Conversion Procedure==

You do not need this procedure to make AlphaFold Server .cif files compatible with FirstGlance in Jmol (see above). You can drop those .cif files directly into the [http://firstglance.jmol.org FrontDoor of FirstGlance].

The procedure below could be used, for example, to convert molecular models in XYZ format to PDB format. Most* CIF-only models from the [[wwPDB]] can also be converted (see ''Caution'' below).
<ol>
<li> Get the Jmol.jar Java application running on your computer by following the instructions at [[Jmol/Application]].
<li> Create a working folder (directory), and put Jmol.jar in it.
<li> Get the .cif file to convert. If you have downloaded a .cif file from the [[wwPDB]], you can skip the next 3 steps.
<ol type="a">
<li> Download the zip file from the [https://alphafoldserver.com AlphaFold3 Server].
<li> Double-click the zip file to unzip it.
<li> In the newly unzipped folder, find the file with a name ending '''_model_0.cif'''. Drag it into your working folder.<ref name="best">Each job produces 5 .cif files. The file with a name ending   _model_0.cif is one of those with the highest overall [https://alphafoldserver.com/faq pTM quality score]. The pTM quality score is in the corresponding '''_summary_confidences_0.json''' file. Open this file in a [[Help:Plain text editors|text editor]]. Look for the third-from-last line, which begins "ptm": (including the quotes) followed by the overall pTM confidence value. See the FAQ at the [https://alphafoldserver.com AlphaFold3 Server] for how to interpret pTM.</ref>
</ol>
<li> Double-click Jmol.jar to run it.
<li> Drag the .cif file and drop it into the black window of Jmol. The model should appear.
<li> In the white ''Jmol Script Console'', enter the command '''write jobname.pdb''', where ''jobname'' is a unique identifier for this model.
<li> Drag and drop ''jobname.pdb'' into [http://firstglance.jmol.org FirstGlance in Jmol].
</ol>

===Caution: Ligand Names May Be Wrong===

If your .cif file had 5-character ligand codes (instead of or in addition to 3-character ligand codes), conversion will truncate those 5-character codes to their first three characters.
(5-character ligand names were introduced after all 3-character codes were in use.)
For example, the ligand code [https://www.rcsb.org/ligand/A1EJM A1EJM] in [[9l63|9L63]] will be truncated to A1E in the converted PDB file. FirstGlance will handle it correctly except that under ''Ligands and Non-Standard Residues'' (in the Molecule Information Tab), '''the link (=?) will display the wrong chemical structure'''; namely, it will display ligand A1E instead of A1EJM.

To display the chemical structure of a ligand with a 5-character code, go to [http://rcsb.org RCSB.org] and enter the 5-character code into the search slot at the top, then press Enter.

To list all the ligand codes in your .cif file, after dropping the .cif file into the black window of Jmol.jar, enter these two '''bold commands''' in the white window (example is [[9dos]]):

<br>
<span style="color:magenta;">$</span> '''select hetero'''
<br>
94 atoms selected
<br>
<span style="color:magenta;">$</span> '''show residues'''
<br>
<span style="color:blue;">[GOL]501:A
<br>
[A1A8V]502:A
<br>
[A1A8V]501:B
<br>
[A1A8V]501:C
<br>
[A1A8V]501:D</span>

GOL is a 3-character ligand code (for glycerol), and A1A8V is a 5-character ligand code. "501:D" means residue number 501 in chain D.

==See Also==
*[[How to predict structures with AlphaFold]]
*[[AlphaFold/Index]]

==Notes==

<references />

Converting AlphaFold3 CIF to PDB

2026-08-18T18:28:08Z

Eric Martz:

The [https://alphafoldserver.com AlphaFold3 Server] predicts models only in the [[Mmcif format|mmCIF format]] (filename ending '''.cif'''). These files<ref name="best">Each job produces 5 .cif files. The file with a name ending   _model_0.cif is one of those with the highest overall [https://alphafoldserver.com/faq pTM quality score]. The pTM quality score is in the corresponding '''_summary_confidences_0.json''' file. Open this file in a [[Help:Plain text editors|text editor]]. Look for the third-from-last line, which begins "ptm": (including the quotes) followed by the overall pTM confidence value. See the FAQ at the [https://alphafoldserver.com AlphaFold3 Server] for how to interpret pTM.</ref> can be visualized & analyzed using ''FirstGlance in Jmol '''version 4.6''''' available via '''[http://firstglance.jmol.org firstglance.jmol.org]'''. These mmCIF files can also be uploaded to [[iCn3D]], or displayed in [[PyMOL]] or [[ChimeraX]].

Only [http://firstglance.jmol.org FirstGlance in Jmol] and [[iCn3D]] automatically color AlphaFold-predicted models by confidence/[[pLDDT]] correctly ('''{{Font color|blue|blue for high confidence}}, {{Font color|red|red for low confidence}}'''). See [[How_to_predict_structures_with_AlphaFold#Visualizing_Predicted_Structures|Visualizing Predicted Structures]].

FirstGlance also makes it [[FirstGlance/How to get average pLDDT from AlphaFold models|easy to get the average pLDDT]] for any range of residues that you specify.

The original version of this article discussed a method for converting AlphaFold 3 .cif models to .pdb format. ''''That is no longer necessary.'''' ''FirstGlance in Jmol '''version 4.6''''' accepts AlphaFold 3 .cif files directly via drag and drop.

About 5% of the models in the [[wwPDB]] are available only in mmCIF format ("CIF-only"). These are more complicated than AlphaFold models, and are not yet supported by FirstGlance. Support is expected later in 2026.

==Conversion Procedure==

You do not need this procedure to make AlphaFold Server .cif files compatible with FirstGlance in Jmol (see above). You can drop those .cif files directly into the [http://firstglance.jmol.org FrontDoor of FirstGlance].

The procedure below could be used, for example, to convert molecular models in XYZ format to PDB format. Most* CIF-only models from the [[wwPDB]] can also be converted (see ''Caution'' below).
<ol>
<li> Get the Jmol.jar Java application running on your computer by following the instructions at [[Jmol/Application]].
<li> Create a working folder (directory), and put Jmol.jar in it.
<li> Get the .cif file to convert. If you have downloaded a .cif file from the [[wwPDB]], you can skip the next 3 steps.
<ol type="a">
<li> Download the zip file from the [https://alphafoldserver.com AlphaFold3 Server].
<li> Double-click the zip file to unzip it.
<li> In the newly unzipped folder, find the file with a name ending '''_model_0.cif'''. Drag it into your working folder.<ref name="best">Each job produces 5 .cif files. The file with a name ending   _model_0.cif is one of those with the highest overall [https://alphafoldserver.com/faq pTM quality score]. The pTM quality score is in the corresponding '''_summary_confidences_0.json''' file. Open this file in a [[Help:Plain text editors|text editor]]. Look for the third-from-last line, which begins "ptm": (including the quotes) followed by the overall pTM confidence value. See the FAQ at the [https://alphafoldserver.com AlphaFold3 Server] for how to interpret pTM.</ref>
</ol>
<li> Double-click Jmol.jar to run it.
<li> Drag the .cif file and drop it into the black window of Jmol. The model should appear.
<li> In the white ''Jmol Script Console'', enter the command '''write jobname.pdb''', where ''jobname'' is a unique identifier for this model.
<li> Drag and drop ''jobname.pdb'' into [http://firstglance.jmol.org FirstGlance in Jmol].
</ol>

===Caution: Ligand Names May Be Wrong===

If your .cif file had 5-character ligand codes (instead of or in addition to 3-character ligand codes), conversion will truncate those 5-character codes to their first three characters.
(5-character ligand names were introduced after all 3-character codes were in use.)
For example, the ligand code [https://www.rcsb.org/ligand/A1EJM A1EJM] in [[9l63|9L63]] will be truncated to A1E in the converted PDB file. FirstGlance will handle it correctly except that under ''Ligands and Non-Standard Residues'' (in the Molecule Information Tab), '''the link (=?) will display the wrong chemical structure'''; namely, it will display ligand A1E instead of A1EJM.

To display the chemical structure of a ligand with a 5-character code, go to [http://rcsb.org RCSB.org] and enter the 5-character code into the search slot at the top, then press Enter.

To list all the ligand codes in your .cif file, after dropping the .cif file into the black window of Jmol.jar, enter these two '''bold commands''' in the white window (example is [[9dos]]):

<br>
<span style="color:magenta;">$</span> '''select hetero'''
<br>
94 atoms selected
<br>
<span style="color:magenta;">$</span> '''show residues'''
<br>
<span style="color:blue;">[GOL]501:A
<br>
[A1A8V]502:A
<br>
[A1A8V]501:B
<br>
[A1A8V]501:C
<br>
[A1A8V]501:D</span>

GOL is a 3-character ligand code (for glycerol), and A1A8V is a 5-character ligand code. "501:D" means residue number 501 in chain D.

==See Also==
*[[How to predict structures with AlphaFold]]
*[[AlphaFold/Index]]

==Notes==

<references />

User talk:Maya M. Morsch

2026-08-03T16:38:49Z

Eric Martz: Welcome!

User:Maya M. Morsch

2026-08-03T16:38:49Z

Eric Martz: Creating user page for new user.

* Full Real Name: Maya M. Morsch

* Position: Student

* Institution (NO ABBREVIATIONS): Hochschule Bremen - City University of Applied Sciences

* City, State/Province: Bremen

* Country: Germany

* Field of Expertise or Study: Biology

* ORCID ID:0009-0007-8887-5491

(ORCID, the Open Researcher and Contributor ID, is a free, unique, persistent identifier https://orcid.org)

Hydrogen in macromolecular models

2026-08-01T18:37:07Z

Eric Martz:

[[Image:Protein Hydrogens in electron Density 1yk4 Y13.jpg|thumb|left|320px|Experimental difference density peaks for hydrogen atoms at 0.69A resolution: [[1yk4]] Tyr 13]]
Approximately 50% of the atoms in a protein are hydrogen. However, hydrogen atoms are absent from most molecular models. Most crystals do not have sufficient [[resolution]] (1.0 Ångstroms or better is needed) to determine the positions of hydrogen atoms directly. It is easy to add hydrogens to macromolecular models, but the results are only as good as the molecular models themselves.

==Absence of Hydrogen Atoms in Most Macromolecular Models==

Hydrogen atoms are absent from most molecular models in Proteopedia, which come mostly from the [[Protein Data Bank]]. 83% of models in the [[Protein Data Bank]] lack hydrogen atoms (in May, 2024). This is because most macromolecular crystals do not have sufficient [[resolution]] to determine the positions of hydrogen atoms. However it is easy to [[#Adding Hydrogens|add hydrogen atoms]], and in fact it is a good idea, because it [[#Model Validation??|helps to correct and validate]] the molecular model.

Although their positions are not well defined empirically in the electron density maps from typical macromolecular crystals, sometimes [[#Adding Hydrogens|hydrogens are added]] to X-ray crystallographic models before they are deposited in the Protein Data Bank. This is the choice of the authors of the [[PDB file]]. Hydrogens are usually present in PDB files resulting from [[NMR]] analysis, and usually present in [[theoretical models]].

==Approximately 50% of Protein Atoms, and approximately 35% of Nucleic Acid Atoms, are Hydrogen==

In proteins, the average number of hydrogens per non-hydrogen atom, weighted to take into account the frequencies of amino acids, is 1.01. Thus, hydrogens are ~50% of all atoms in protein. Nucleic acids have fewer, ~35%.

To '''determine the percentage of atoms that are hydrogen''' in a model in Proteopedia, click on the word ''Jmol'' in the lower right corner of the rotatable molecular scene, and then on ''Console''. In the lower box of the Console window that opens, enter "select hydrogen" and note the atom count in the report in the upper box. Then do the same for "select not hydrogen".

To '''visualize hydrogen atoms''', use the ''FirstGlance'' link in the ''Resources'' section beneath the molecular scene. Once the model is displayed in [[FirstGlance in Jmol]], click on ''Vines''. Change the background to black with the background toggle button. Now click on ''Vines''. In the help panel for ''Vines'', check ''More detail''. Hydrogen atoms are white. To hide and then show them, check ''Hide hydrogens'', then uncheck it.

<blockquote>
The value 1.01, for the average number of protein hydrogens per non-hydrogen protein atom, was calculated from the values for each amino acid, weighted by average frequencies of amino acids. The frequencies employed are based on 1,021 unrelated proteins of known sequence, tabulated on page 5 in Creighton (1993)<ref>"Proteins, Structures and Molecular Properties", Thomas E. Creighton, 2nd ed., 1993, W. H. Freeman and Co.</ref>.
</blockquote>

==Hydrogens Present in Macromolecular Models==

===Empirically-Positioned Hydrogens in High-Resolution Crystallographic Models===

High [[resolution]] protein crystallography (1.2 Ångstroms or better) can assign some hydrogen positions empirically from the electron density map, and very high resolution crystals (1.0 Ångstroms or better) can assign the positions of most hydrogens.

* '''Example:''' The X-ray model of a tyrosine kinase SH2 domain [[1lkk]] at 1.0 Angstrom resolution contains 901 hydrogens and 920 non-hydrogen protein atoms (ratio 0.98, 49%), so approximately all of the hydrogens actually present are assigned positions.

===Theoretically-Positioned Hydrogens in Average-Resolution Crystallographic Models===

As explained above, most macromolecular crystals do not provide high enough resolution to detect hydrogen positions empirically. The median [[resolution]] of models in the [[Protein Data Bank]] is 2.0 Å.

*'''Example: No hydrogens''': The X-ray model in PDB file [[1hho]] for oxyhemoglobin (2.1 A resolution) contains no hydrogens.

*'''Example: Some hydrogens from theory''': The X-ray file [[1lfa]] (1.8 A resolution; an integrin adhesion protein domain) contains 312 waters each with 2 hydrogens (so 624 water hydrogens), plus 639 protein hydrogens for 2,939 non-hydrogen protein atoms, which account for only about 22% (639/~2,939) of the hydrogens actually present in this protein. The protein hydrogens in the model are the polar hydrogens: one hydrogen on each main chain nitrogen (three hydrogens/amino terminal nitrogen), and hydrogens on sidechain oxygens or nitrogens in Ser, Thr, Tyr, Lys, Arg, His, Asn, and Gln. None of the hydrogens covalently bonded to carbons are present. The hydrogens which are present are required for the molecular dynamics stages of refinement of the X-ray model in the popular crystallographic refinement program X-PLOR; some authors strip them out before submitting a [[PDB file]] and others leave them in. The [[Protein Data Bank]] accepts X-ray models either way, according to the preference of the depositor.

*'''Example: All hydrogens from theory''': [[4gl2]], a 2013 [[X-ray crystallographic]] model of a protein-RNA complex, has all hydrogens, yet at its [[resolution]] of 3.56 Å, no hydrogens could have been resolved in the electron density map.

===Hydrogens in NMR Models===

[[NMR]] methods also determine some hydrogen positions. Typically all hydrogens are modeled in before the molecule is folded to fit the NMR interatomic distance restraints; hence, all hydrogens are usually present in NMR models submitted to the PDB.

*'''Example:''' The calmodulin ensemble of 25 [[NMR]] models [[1cfc]] contains 1096 protein hydrogens and 1166 non-hydrogen protein atoms per model (ratio 0.94, 48.5%), thereby assigning positions for approximately all of the hydrogens actually present.
*'''Example:''' The lac repressor:DNA complex ensemble of 3 [[NMR]] models [[1lcd]] contains 294 protein hydrogens and 1197 non-hydrogen protein atoms per model (ratio 0.25, 19.7%). Only the polar protein hydrogens are present in this model. There are 141 hydrogens in the DNA, and 1,335 non-hydrogen DNA atoms (9.6%). Only the Watson-Crick and terminal deoxyribose hydrogens are present. All 138 water molecules are modeled as H<sub>2</sub>O. Individual models contain 243, 235, and 233 hydrogens. (Author E.M. did not determine the basis for these differences.)

==Adding Hydrogens From Theory==

It is easy to add hydrogens to macromolecular models ([[PDB files]]) using the highly-reliable free programs listed below. Beware that the results are only as good as the molecular models themselves. Uncertainties in the positions of non-hydrogen atoms will, of course, produce inaccurate positions for hydrogen atoms. In fact, the quality of the molecular model can be judged in part from how well the hydrogens fit into the spaces between the non-hydrogen atoms. This degree of fit is quantitated in the ''overall clash score'' reported by the first method below, ''Molprobity''.

* Use the Richardson Lab's easy and very powerful [http://molprobity.biochem.duke.edu/ MolProbity: All-Atom Contact Analysis] server. Hydrogens are added to both protein and nucleic acids (but not to water), and you can save the resulting [[PDB file]]. This server has the advantage that you also get a powerful analysis of the quality of the model, including which Gln/Asn/His residues should have their sidechains flipped, an overall clash score, etc. You can save a model with the recommended sidechains flipped. Also you can visualize clashes anywhere in the model, including with the sidechains flipped or not flipped.

* Use the Vriend Lab's [https://swift.cmbi.umcn.nl/servers/html/index.html WHATIF WWW Interface]. Hydrogens are added to both protein and nucleic acids '''and also to water'''.
**Under Classes (at left) click "Hydrogen (bonds)".
**Select "Add protons to the structure".
**Enter your PDB ID or upload a coordinate file.
**After the results appear, click on the pdb link to receive the coordinate file containing added hydrogens.

* Use the free [[Jmol/Application|Jmol Application]]. Enter these commands in the white ''Jmol Script Console'' window:
** [https://chemapps.stolaf.edu/jmol/docs/#k1188 set pdbAddHydrogens true]
**[[Jmol/Application#Loading_a_Molecule|Load the molecule]] (must be done AFTER the previous command).
** select all (only the selected atoms will be written)
** write hadded.pdb ("hadded" can be your filename, but must end ".pdb")

[[PDB files]] that you save from either of these methods, can, for example, be dropped into [[FirstGlance in Jmol]] for visualization and analysis.

===Test Results===

[[1d66]] is an early (1992) modest resolution (2.7 Å) crystallographic model containing protein, DNA and 51 water oxygens. MolProbity reports its clashscore as 11.7, 65th percentile. The model deposited in the [[PDB]] contains no hydrogen atoms.

{| class="wikitable" style="text-align:right"
|+ Results for 1d66
! Program !! Protein Hydrogens !! Nucleic Hydrogens !! Water Hydrogens !! Total Hydrogens
|-
| MolProbity || 982 || 427 || 0 || 1,409
|-
| WHATIF || 1,000 || 423 || 102 || 1,525
|-
| Jmol || 990 || 427 || 0 || 1,417
|}
'''1d66:''' WHATIF protonated the sulfurs in 12 cysteines that are coordinating 4 cadmium ions; Molprobity and Jmol did not. WHATIF and Jmol protonated the 2 N terminal protein nitrogens (6 H atoms), while MolProbity did not. MolProbity and Jmol protonated the terminal hydroxyls on the 2 DNA chains, while WHATIF did not. All hydrogens added by MolProbity appeared to be in reasonable geometries, while some of those added by WHATIF were not.

MolProbity and WHATIF were tested in 2008. Jmol was tested in 2026.

==See Also==
*[[Hydrogen bonds]]
*[[Resolution]]
*[[Quality assessment for molecular models]]
*[[Water in macromolecular models]]

==Content Attribution==

Most of the original content in this article was adapted, with permission, from documentation written earlier by [[User:Eric Martz]], for several locations in [[Protein Explorer]]: [http://proteinexplorer.org/iv_water.htm Water], [http://proteinexplorer.org/help_hyd.htm Hydrogens in PDB files], and ''Hydrogen'' in the [http://proteinexplorer.org/igloss.htm Help/Index/Glossary].

Thanks to John Badger for key contributions.

==Notes & References==
<references />

[[Category:Topic Page]]

Hydrogen in macromolecular models

2026-08-01T18:33:30Z

Eric Martz:

[[Image:Protein Hydrogens in electron Density 1yk4 Y13.jpg|thumb|left|320px|Experimental difference density peaks for hydrogen atoms at 0.69A resolution: [[1yk4]] Tyr 13]]
Approximately 50% of the atoms in a protein are hydrogen. However, hydrogen atoms are absent from most molecular models. Most crystals do not have sufficient [[resolution]] (1.0 Ångstroms or better is needed) to determine the positions of hydrogen atoms directly. It is easy to add hydrogens to macromolecular models, but the results are only as good as the molecular models themselves.

==Absence of Hydrogen Atoms in Most Macromolecular Models==

Hydrogen atoms are absent from most molecular models in Proteopedia, which come mostly from the [[Protein Data Bank]]. 83% of models in the [[Protein Data Bank]] lack hydrogen atoms (in May, 2024). This is because most macromolecular crystals do not have sufficient [[resolution]] to determine the positions of hydrogen atoms. However it is easy to [[#Adding Hydrogens|add hydrogen atoms]], and in fact it is a good idea, because it [[#Model Validation??|helps to correct and validate]] the molecular model.

Although their positions are not well defined empirically in the electron density maps from typical macromolecular crystals, sometimes [[#Adding Hydrogens|hydrogens are added]] to X-ray crystallographic models before they are deposited in the Protein Data Bank. This is the choice of the authors of the [[PDB file]]. Hydrogens are usually present in PDB files resulting from [[NMR]] analysis, and usually present in [[theoretical models]].

==Approximately 50% of Protein Atoms, and approximately 35% of Nucleic Acid Atoms, are Hydrogen==

In proteins, the average number of hydrogens per non-hydrogen atom, weighted to take into account the frequencies of amino acids, is 1.01. Thus, hydrogens are ~50% of all atoms in protein. Nucleic acids have fewer, ~35%.

To '''determine the percentage of atoms that are hydrogen''' in a model in Proteopedia, click on the word ''Jmol'' in the lower right corner of the rotatable molecular scene, and then on ''Console''. In the lower box of the Console window that opens, enter "select hydrogen" and note the atom count in the report in the upper box. Then do the same for "select not hydrogen".

To '''visualize hydrogen atoms''', use the ''FirstGlance'' link in the ''Resources'' section beneath the molecular scene. Once the model is displayed in [[FirstGlance in Jmol]], click on ''Vines''. Change the background to black with the background toggle button. Now click on ''Vines''. In the help panel for ''Vines'', check ''More detail''. Hydrogen atoms are white. To hide and then show them, check ''Hide hydrogens'', then uncheck it.

<blockquote>
The value 1.01, for the average number of protein hydrogens per non-hydrogen protein atom, was calculated from the values for each amino acid, weighted by average frequencies of amino acids. The frequencies employed are based on 1,021 unrelated proteins of known sequence, tabulated on page 5 in Creighton (1993)<ref>"Proteins, Structures and Molecular Properties", Thomas E. Creighton, 2nd ed., 1993, W. H. Freeman and Co.</ref>.
</blockquote>

==Hydrogens Present in Macromolecular Models==

===Empirically-Positioned Hydrogens in High-Resolution Crystallographic Models===

High [[resolution]] protein crystallography (1.2 Ångstroms or better) can assign some hydrogen positions empirically from the electron density map, and very high resolution crystals (1.0 Ångstroms or better) can assign the positions of most hydrogens.

* '''Example:''' The X-ray model of a tyrosine kinase SH2 domain [[1lkk]] at 1.0 Angstrom resolution contains 901 hydrogens and 920 non-hydrogen protein atoms (ratio 0.98, 49%), so approximately all of the hydrogens actually present are assigned positions.

===Theoretically-Positioned Hydrogens in Average-Resolution Crystallographic Models===

As explained above, most macromolecular crystals do not provide high enough resolution to detect hydrogen positions empirically. The median [[resolution]] of models in the [[Protein Data Bank]] is 2.0 Å.

*'''Example: No hydrogens''': The X-ray model in PDB file [[1hho]] for oxyhemoglobin (2.1 A resolution) contains no hydrogens.

*'''Example: Some hydrogens from theory''': The X-ray file [[1lfa]] (1.8 A resolution; an integrin adhesion protein domain) contains 312 waters each with 2 hydrogens (so 624 water hydrogens), plus 639 protein hydrogens for 2,939 non-hydrogen protein atoms, which account for only about 22% (639/~2,939) of the hydrogens actually present in this protein. The protein hydrogens in the model are the polar hydrogens: one hydrogen on each main chain nitrogen (three hydrogens/amino terminal nitrogen), and hydrogens on sidechain oxygens or nitrogens in Ser, Thr, Tyr, Lys, Arg, His, Asn, and Gln. None of the hydrogens covalently bonded to carbons are present. The hydrogens which are present are required for the molecular dynamics stages of refinement of the X-ray model in the popular crystallographic refinement program X-PLOR; some authors strip them out before submitting a [[PDB file]] and others leave them in. The [[Protein Data Bank]] accepts X-ray models either way, according to the preference of the depositor.

*'''Example: All hydrogens from theory''': [[4gl2]], a 2013 [[X-ray crystallographic]] model of a protein-RNA complex, has all hydrogens, yet at its [[resolution]] of 3.56 Å, no hydrogens could have been resolved in the electron density map.

===Hydrogens in NMR Models===

[[NMR]] methods also determine some hydrogen positions. Typically all hydrogens are modeled in before the molecule is folded to fit the NMR interatomic distance restraints; hence, all hydrogens are usually present in NMR models submitted to the PDB.

*'''Example:''' The calmodulin ensemble of 25 [[NMR]] models [[1cfc]] contains 1096 protein hydrogens and 1166 non-hydrogen protein atoms per model (ratio 0.94, 48.5%), thereby assigning positions for approximately all of the hydrogens actually present.
*'''Example:''' The lac repressor:DNA complex ensemble of 3 [[NMR]] models [[1lcd]] contains 294 protein hydrogens and 1197 non-hydrogen protein atoms per model (ratio 0.25, 19.7%). Only the polar protein hydrogens are present in this model. There are 141 hydrogens in the DNA, and 1,335 non-hydrogen DNA atoms (9.6%). Only the Watson-Crick and terminal deoxyribose hydrogens are present. All 138 water molecules are modeled as H<sub>2</sub>O. Individual models contain 243, 235, and 233 hydrogens. (Author E.M. did not determine the basis for these differences.)

==Adding Hydrogens From Theory==

It is easy to add hydrogens to macromolecular models ([[PDB files]]) using the highly-reliable free programs listed below. Beware that the results are only as good as the molecular models themselves. Uncertainties in the positions of non-hydrogen atoms will, of course, produce inaccurate positions for hydrogen atoms. In fact, the quality of the molecular model can be judged in part from how well the hydrogens fit into the spaces between the non-hydrogen atoms. This degree of fit is quantitated in the ''overall clash score'' reported by the first method below, ''Molprobity''.

* Use the Richardson Lab's easy and very powerful [http://molprobity.biochem.duke.edu/ MolProbity: All-Atom Contact Analysis] server. Hydrogens are added to both protein and nucleic acids (but not to water), and you can save the resulting [[PDB file]]. This server has the advantage that you also get a powerful analysis of the quality of the model, including which Gln/Asn/His residues should have their sidechains flipped, an overall clash score, etc. You can save a model with the recommended sidechains flipped. Also you can visualize clashes anywhere in the model, including with the sidechains flipped or not flipped.

* Use the Vriend Lab's [https://swift.cmbi.umcn.nl/servers/html/index.html WHATIF WWW Interface]. Hydrogens are added to both protein and nucleic acids '''and also to water'''.
**Under Classes (at left) click "Hydrogen (bonds)".
**Select "Add protons to the structure".
**Enter your PDB ID or upload a coordinate file.
**After the results appear, click on the pdb link to receive the coordinate file containing added hydrogens.

* Use the free [[Jmol/Application|Jmol Application]]. Enter these commands in the white ''Jmol Script Console'' window:
** set pdbAddHydrogens true
**[[Jmol/Application#Loading_a_Molecule|Load the molecule]] (must be done AFTER the previous command).
** select all (only the selected atoms will be written)
** write hadded.pdb ("hadded" can be your filename, but must end ".pdb")

[[PDB files]] that you save from either of these methods, can, for example, be dropped into [[FirstGlance in Jmol]] for visualization and analysis.

===Test Results===

[[1d66]] is an early (1992) modest resolution (2.7 Å) crystallographic model containing protein, DNA and 51 water oxygens. MolProbity reports its clashscore as 11.7, 65th percentile. The model deposited in the [[PDB]] contains no hydrogen atoms.

{| class="wikitable" style="text-align:right"
|+ Results for 1d66
! Program !! Protein Hydrogens !! Nucleic Hydrogens !! Water Hydrogens !! Total Hydrogens
|-
| MolProbity || 982 || 427 || 0 || 1,409
|-
| WHATIF || 1,000 || 423 || 102 || 1,525
|-
| Jmol || 990 || 427 || 0 || 1,417
|}
'''1d66:''' WHATIF protonated the sulfurs in 12 cysteines that are coordinating 4 cadmium ions; Molprobity and Jmol did not. WHATIF and Jmol protonated the 2 N terminal protein nitrogens (6 H atoms), while MolProbity did not. MolProbity and Jmol protonated the terminal hydroxyls on the 2 DNA chains, while WHATIF did not. All hydrogens added by MolProbity appeared to be in reasonable geometries, while some of those added by WHATIF were not.

MolProbity and WHATIF were tested in 2008. Jmol was tested in 2026.

==See Also==
*[[Hydrogen bonds]]
*[[Resolution]]
*[[Quality assessment for molecular models]]
*[[Water in macromolecular models]]

==Content Attribution==

Most of the original content in this article was adapted, with permission, from documentation written earlier by [[User:Eric Martz]], for several locations in [[Protein Explorer]]: [http://proteinexplorer.org/iv_water.htm Water], [http://proteinexplorer.org/help_hyd.htm Hydrogens in PDB files], and ''Hydrogen'' in the [http://proteinexplorer.org/igloss.htm Help/Index/Glossary].

Thanks to John Badger for key contributions.

==Notes & References==
<references />

[[Category:Topic Page]]

Hydrogen in macromolecular models

2026-08-01T18:20:19Z

Eric Martz:

[[Image:Protein Hydrogens in electron Density 1yk4 Y13.jpg|thumb|left|320px|Experimental difference density peaks for hydrogen atoms at 0.69A resolution: [[1yk4]] Tyr 13]]
Approximately 50% of the atoms in a protein are hydrogen. However, hydrogen atoms are absent from most molecular models. Most crystals do not have sufficient [[resolution]] (1.0 Ångstroms or better is needed) to determine the positions of hydrogen atoms directly. It is easy to add hydrogens to macromolecular models, but the results are only as good as the molecular models themselves.

==Absence of Hydrogen Atoms in Most Macromolecular Models==

Hydrogen atoms are absent from most molecular models in Proteopedia, which come mostly from the [[Protein Data Bank]]. 83% of models in the [[Protein Data Bank]] lack hydrogen atoms (in May, 2024). This is because most macromolecular crystals do not have sufficient [[resolution]] to determine the positions of hydrogen atoms. However it is easy to [[#Adding Hydrogens|add hydrogen atoms]], and in fact it is a good idea, because it [[#Model Validation??|helps to correct and validate]] the molecular model.

Although their positions are not well defined empirically in the electron density maps from typical macromolecular crystals, sometimes [[#Adding Hydrogens|hydrogens are added]] to X-ray crystallographic models before they are deposited in the Protein Data Bank. This is the choice of the authors of the [[PDB file]]. Hydrogens are usually present in PDB files resulting from [[NMR]] analysis, and usually present in [[theoretical models]].

==Approximately 50% of Protein Atoms, and approximately 35% of Nucleic Acid Atoms, are Hydrogen==

In proteins, the average number of hydrogens per non-hydrogen atom, weighted to take into account the frequencies of amino acids, is 1.01. Thus, hydrogens are ~50% of all atoms in protein. Nucleic acids have fewer, ~35%.

To '''determine the percentage of atoms that are hydrogen''' in a model in Proteopedia, click on the word ''Jmol'' in the lower right corner of the rotatable molecular scene, and then on ''Console''. In the lower box of the Console window that opens, enter "select hydrogen" and note the atom count in the report in the upper box. Then do the same for "select not hydrogen".

To '''visualize hydrogen atoms''', use the ''FirstGlance'' link in the ''Resources'' section beneath the molecular scene. Once the model is displayed in [[FirstGlance in Jmol]], click on ''Vines''. Change the background to black with the background toggle button. Now click on ''Vines''. In the help panel for ''Vines'', check ''More detail''. Hydrogen atoms are white. To hide and then show them, check ''Hide hydrogens'', then uncheck it.

<blockquote>
The value 1.01, for the average number of protein hydrogens per non-hydrogen protein atom, was calculated from the values for each amino acid, weighted by average frequencies of amino acids. The frequencies employed are based on 1,021 unrelated proteins of known sequence, tabulated on page 5 in Creighton (1993)<ref>"Proteins, Structures and Molecular Properties", Thomas E. Creighton, 2nd ed., 1993, W. H. Freeman and Co.</ref>.
</blockquote>

==Hydrogens Present in Macromolecular Models==

===Empirically-Positioned Hydrogens in High-Resolution Crystallographic Models===

High [[resolution]] protein crystallography (1.2 Ångstroms or better) can assign some hydrogen positions empirically from the electron density map, and very high resolution crystals (1.0 Ångstroms or better) can assign the positions of most hydrogens.

* '''Example:''' The X-ray model of a tyrosine kinase SH2 domain [[1lkk]] at 1.0 Angstrom resolution contains 901 hydrogens and 920 non-hydrogen protein atoms (ratio 0.98, 49%), so approximately all of the hydrogens actually present are assigned positions.

===Theoretically-Positioned Hydrogens in Average-Resolution Crystallographic Models===

As explained above, most macromolecular crystals do not provide high enough resolution to detect hydrogen positions empirically. The median [[resolution]] of models in the [[Protein Data Bank]] is 2.0 Å.

*'''Example: No hydrogens''': The X-ray model in PDB file [[1hho]] for oxyhemoglobin (2.1 A resolution) contains no hydrogens.

*'''Example: Some hydrogens from theory''': The X-ray file [[1lfa]] (1.8 A resolution; an integrin adhesion protein domain) contains 312 waters each with 2 hydrogens (so 624 water hydrogens), plus 639 protein hydrogens for 2,939 non-hydrogen protein atoms, which account for only about 22% (639/~2,939) of the hydrogens actually present in this protein. The protein hydrogens in the model are the polar hydrogens: one hydrogen on each main chain nitrogen (three hydrogens/amino terminal nitrogen), and hydrogens on sidechain oxygens or nitrogens in Ser, Thr, Tyr, Lys, Arg, His, Asn, and Gln. None of the hydrogens covalently bonded to carbons are present. The hydrogens which are present are required for the molecular dynamics stages of refinement of the X-ray model in the popular crystallographic refinement program X-PLOR; some authors strip them out before submitting a [[PDB file]] and others leave them in. The [[Protein Data Bank]] accepts X-ray models either way, according to the preference of the depositor.

*'''Example: All hydrogens from theory''': [[4gl2]], a 2013 [[X-ray crystallographic]] model of a protein-RNA complex, has all hydrogens, yet at its [[resolution]] of 3.56 Å, no hydrogens could have been resolved in the electron density map.

===Hydrogens in NMR Models===

[[NMR]] methods also determine some hydrogen positions. Typically all hydrogens are modeled in before the molecule is folded to fit the NMR interatomic distance restraints; hence, all hydrogens are usually present in NMR models submitted to the PDB.

*'''Example:''' The calmodulin ensemble of 25 [[NMR]] models [[1cfc]] contains 1096 protein hydrogens and 1166 non-hydrogen protein atoms per model (ratio 0.94, 48.5%), thereby assigning positions for approximately all of the hydrogens actually present.
*'''Example:''' The lac repressor:DNA complex ensemble of 3 [[NMR]] models [[1lcd]] contains 294 protein hydrogens and 1197 non-hydrogen protein atoms per model (ratio 0.25, 19.7%). Only the polar protein hydrogens are present in this model. There are 141 hydrogens in the DNA, and 1,335 non-hydrogen DNA atoms (9.6%). Only the Watson-Crick and terminal deoxyribose hydrogens are present. All 138 water molecules are modeled as H<sub>2</sub>O. Individual models contain 243, 235, and 233 hydrogens. (Author E.M. did not determine the basis for these differences.)

==Adding Hydrogens From Theory==

It is easy to add hydrogens to macromolecular models ([[PDB files]]) using the highly-reliable free programs listed below. Beware that the results are only as good as the molecular models themselves. Uncertainties in the positions of non-hydrogen atoms will, of course, produce inaccurate positions for hydrogen atoms. In fact, the quality of the molecular model can be judged in part from how well the hydrogens fit into the spaces between the non-hydrogen atoms. This degree of fit is quantitated in the ''overall clash score'' reported by the first method below, ''Molprobity''.

* Use the Richardson Lab's easy and very powerful [http://molprobity.biochem.duke.edu/ MolProbity: All-Atom Contact Analysis] server. Hydrogens are added to both protein and nucleic acids (but not to water), and you can save the resulting [[PDB file]]. This server has the advantage that you also get a powerful analysis of the quality of the model, including which Gln/Asn/His residues should have their sidechains flipped, an overall clash score, etc. You can save a model with the recommended sidechains flipped. Also you can visualize clashes anywhere in the model, including with the sidechains flipped or not flipped.

* Use the Vriend Lab's [https://swift.cmbi.umcn.nl/servers/html/index.html WHATIF WWW Interface]. Hydrogens are added to both protein and nucleic acids '''and also to water'''.
**Under Classes (at left) click "Hydrogen (bonds)".
**Select "Add protons to the structure".
**Enter your PDB ID or upload a coordinate file.
**After the results appear, click on the pdb link to receive the coordinate file containing added hydrogens.

* Use the free [[Jmol/Application|Jmol Application]]. Enter these commands in the white ''Jmol Script Console'' window:
** set pdbAddHydrogens true
**[[Jmol/Application#Loading_a_Molecule|Load the molecule]] (must be done AFTER the previous command).
** select all (only the selected atoms will be written)
** write hadded.pdb ("hadded" can be your filename, but must end ".pdb")

[[PDB files]] that you save from either of these methods, can, for example, be dropped into [[FirstGlance in Jmol]] for visualization and analysis.

===Test Results===

[[1d66]] is an early (1992) modest resolution (2.7 Å) crystallographic model containing protein, DNA and 51 water oxygens. MolProbity reports its clashscore as 11.7, 65th percentile. The model deposited in the [[PDB]] contains no hydrogen atoms.

{| class="wikitable" style="text-align:right"
|+ Results for 1d66
! Program !! Protein Hydrogens !! Nucleic Hydrogens !! Water Hydrogens !! Total Hydrogens
|-
| MolProbity || 982 || 427 || 0 || 1,409
|-
| WHATIF || 1,000 || 423 || 102 || 1,525
|-
| Jmol || 990 || 427 || 0 || 1,417
|}
'''1d66:''' WHATIF protonates the sulfurs in 12 cysteines that are coordinating 4 cadmium ions, and the 2 N terminal nitrogens (6 H atoms), while MolProbity does not. MolProbity protonates the terminal hydroxyls on the 2 DNA chains, while WHATIF does not. All hydrogens added by MolProbity appeared to be in reasonable geometries, while some of those added by WHATIF were not.

MolProbity and WHATIF were tested in 2008. Jmol was tested in 2026.

==See Also==
*[[Hydrogen bonds]]
*[[Resolution]]
*[[Quality assessment for molecular models]]
*[[Water in macromolecular models]]

==Content Attribution==

Most of the original content in this article was adapted, with permission, from documentation written earlier by [[User:Eric Martz]], for several locations in [[Protein Explorer]]: [http://proteinexplorer.org/iv_water.htm Water], [http://proteinexplorer.org/help_hyd.htm Hydrogens in PDB files], and ''Hydrogen'' in the [http://proteinexplorer.org/igloss.htm Help/Index/Glossary].

Thanks to John Badger for key contributions.

==Notes & References==
<references />

[[Category:Topic Page]]

Hydrogen in macromolecular models

2026-08-01T18:17:00Z

Eric Martz:

[[Image:Protein Hydrogens in electron Density 1yk4 Y13.jpg|thumb|left|320px|Experimental difference density peaks for hydrogen atoms at 0.69A resolution: [[1yk4]] Tyr 13]]
Approximately 50% of the atoms in a protein are hydrogen. However, hydrogen atoms are absent from most molecular models. Most crystals do not have sufficient [[resolution]] (1.0 Ångstroms or better is needed) to determine the positions of hydrogen atoms directly. It is easy to add hydrogens to macromolecular models, but the results are only as good as the molecular models themselves.

==Absence of Hydrogen Atoms in Most Macromolecular Models==

Hydrogen atoms are absent from most molecular models in Proteopedia, which come mostly from the [[Protein Data Bank]]. 83% of models in the [[Protein Data Bank]] lack hydrogen atoms (in May, 2024). This is because most macromolecular crystals do not have sufficient [[resolution]] to determine the positions of hydrogen atoms. However it is easy to [[#Adding Hydrogens|add hydrogen atoms]], and in fact it is a good idea, because it [[#Model Validation??|helps to correct and validate]] the molecular model.

Although their positions are not well defined empirically in the electron density maps from typical macromolecular crystals, sometimes [[#Adding Hydrogens|hydrogens are added]] to X-ray crystallographic models before they are deposited in the Protein Data Bank. This is the choice of the authors of the [[PDB file]]. Hydrogens are usually present in PDB files resulting from [[NMR]] analysis, and usually present in [[theoretical models]].

==Approximately 50% of Protein Atoms, and approximately 35% of Nucleic Acid Atoms, are Hydrogen==

In proteins, the average number of hydrogens per non-hydrogen atom, weighted to take into account the frequencies of amino acids, is 1.01. Thus, hydrogens are ~50% of all atoms in protein. Nucleic acids have fewer, ~35%.

To '''determine the percentage of atoms that are hydrogen''' in a model in Proteopedia, click on the word ''Jmol'' in the lower right corner of the rotatable molecular scene, and then on ''Console''. In the lower box of the Console window that opens, enter "select hydrogen" and note the atom count in the report in the upper box. Then do the same for "select not hydrogen".

To '''visualize hydrogen atoms''', use the ''FirstGlance'' link in the ''Resources'' section beneath the molecular scene. Once the model is displayed in [[FirstGlance in Jmol]], click on ''Vines''. Change the background to black with the background toggle button. Now click on ''Vines''. In the help panel for ''Vines'', check ''More detail''. Hydrogen atoms are white. To hide and then show them, check ''Hide hydrogens'', then uncheck it.

<blockquote>
The value 1.01, for the average number of protein hydrogens per non-hydrogen protein atom, was calculated from the values for each amino acid, weighted by average frequencies of amino acids. The frequencies employed are based on 1,021 unrelated proteins of known sequence, tabulated on page 5 in Creighton (1993)<ref>"Proteins, Structures and Molecular Properties", Thomas E. Creighton, 2nd ed., 1993, W. H. Freeman and Co.</ref>.
</blockquote>

==Hydrogens Present in Macromolecular Models==

===Empirically-Positioned Hydrogens in High-Resolution Crystallographic Models===

High [[resolution]] protein crystallography (1.2 Ångstroms or better) can assign some hydrogen positions empirically from the electron density map, and very high resolution crystals (1.0 Ångstroms or better) can assign the positions of most hydrogens.

* '''Example:''' The X-ray model of a tyrosine kinase SH2 domain [[1lkk]] at 1.0 Angstrom resolution contains 901 hydrogens and 920 non-hydrogen protein atoms (ratio 0.98, 49%), so approximately all of the hydrogens actually present are assigned positions.

===Theoretically-Positioned Hydrogens in Average-Resolution Crystallographic Models===

As explained above, most macromolecular crystals do not provide high enough resolution to detect hydrogen positions empirically. The median [[resolution]] of models in the [[Protein Data Bank]] is 2.0 Å.

*'''Example: No hydrogens''': The X-ray model in PDB file [[1hho]] for oxyhemoglobin (2.1 A resolution) contains no hydrogens.

*'''Example: Some hydrogens from theory''': The X-ray file [[1lfa]] (1.8 A resolution; an integrin adhesion protein domain) contains 312 waters each with 2 hydrogens (so 624 water hydrogens), plus 639 protein hydrogens for 2,939 non-hydrogen protein atoms, which account for only about 22% (639/~2,939) of the hydrogens actually present in this protein. The protein hydrogens in the model are the polar hydrogens: one hydrogen on each main chain nitrogen (three hydrogens/amino terminal nitrogen), and hydrogens on sidechain oxygens or nitrogens in Ser, Thr, Tyr, Lys, Arg, His, Asn, and Gln. None of the hydrogens covalently bonded to carbons are present. The hydrogens which are present are required for the molecular dynamics stages of refinement of the X-ray model in the popular crystallographic refinement program X-PLOR; some authors strip them out before submitting a [[PDB file]] and others leave them in. The [[Protein Data Bank]] accepts X-ray models either way, according to the preference of the depositor.

*'''Example: All hydrogens from theory''': [[4gl2]], a 2013 [[X-ray crystallographic]] model of a protein-RNA complex, has all hydrogens, yet at its [[resolution]] of 3.56 Å, no hydrogens could have been resolved in the electron density map.

===Hydrogens in NMR Models===

[[NMR]] methods also determine some hydrogen positions. Typically all hydrogens are modeled in before the molecule is folded to fit the NMR interatomic distance restraints; hence, all hydrogens are usually present in NMR models submitted to the PDB.

*'''Example:''' The calmodulin ensemble of 25 [[NMR]] models [[1cfc]] contains 1096 protein hydrogens and 1166 non-hydrogen protein atoms per model (ratio 0.94, 48.5%), thereby assigning positions for approximately all of the hydrogens actually present.
*'''Example:''' The lac repressor:DNA complex ensemble of 3 [[NMR]] models [[1lcd]] contains 294 protein hydrogens and 1197 non-hydrogen protein atoms per model (ratio 0.25, 19.7%). Only the polar protein hydrogens are present in this model. There are 141 hydrogens in the DNA, and 1,335 non-hydrogen DNA atoms (9.6%). Only the Watson-Crick and terminal deoxyribose hydrogens are present. All 138 water molecules are modeled as H<sub>2</sub>O. Individual models contain 243, 235, and 233 hydrogens. (Author E.M. did not determine the basis for these differences.)

==Adding Hydrogens From Theory==

It is easy to add hydrogens to macromolecular models ([[PDB files]]) using the highly-reliable free servers listed below. Beware that the results are only as good as the molecular models themselves. Uncertainties in the positions of non-hydrogen atoms will, of course, produce inaccurate positions for hydrogen atoms. In fact, the quality of the molecular model can be judged in part from how well the hydrogens fit into the spaces between the non-hydrogen atoms. This degree of fit is quantitated in the ''overall clash score'' reported by the first method below, ''Molprobity''.

* Use the Richardson Lab's easy and very powerful [http://molprobity.biochem.duke.edu/ MolProbity: All-Atom Contact Analysis] server. Hydrogens are added to both protein and nucleic acids (but not to water), and you can save the resulting [[PDB file]]. This server has the advantage that you also get a powerful analysis of the quality of the model, including which Gln/Asn/His residues should have their sidechains flipped, an overall clash score, etc. You can save a model with the recommended sidechains flipped. Also you can visualize clashes anywhere in the model, including with the sidechains flipped or not flipped.

* Use the Vriend Lab's [https://swift.cmbi.umcn.nl/servers/html/index.html WHATIF WWW Interface]. Hydrogens are added to both protein and nucleic acids '''and also to water'''.
**Under Classes (at left) click "Hydrogen (bonds)".
**Select "Add protons to the structure".
**Enter your PDB ID or upload a coordinate file.
**After the results appear, click on the pdb link to receive the coordinate file containing added hydrogens.

* Use the free [[Jmol/Application|Jmol Application]]. Enter these commands in the white ''Jmol Script Console'' window:
** set pdbAddHydrogens true
**[[https://proteopedia.org/w/Jmol/Application#Loading_a_Molecule|Load the molecule]] (must be done AFTER the previous command).
** select all (only the selected atoms will be written)
** write hadded.pdb ("hadded" can be your filename, but must end ".pdb")

[[PDB files]] that you save from either of these methods, can, for example, be uploaded for visualization in [[FirstGlance in Jmol]].

===Test Results===

[[1d66]] is an early (1992) modest resolution (2.7 Å) crystallographic model containing protein, DNA and 51 water oxygens. MolProbity reports its clashscore as 11.7, 65th percentile. The model deposited in the [[PDB]] contains no hydrogen atoms.

{| class="wikitable" style="text-align:right"
|+ Results for 1d66
! Program !! Protein Hydrogens !! Nucleic Hydrogens !! Water Hydrogens !! Total Hydrogens
|-
| MolProbity || 982 || 427 || 0 || 1,409
|-
| WHATIF || 1,000 || 423 || 102 || 1,525
|-
| Jmol || 990 || 427 || 0 || 1,417
|}
'''1d66:''' WHATIF protonates the sulfurs in 12 cysteines that are coordinating 4 cadmium ions, and the 2 N terminal nitrogens (6 H atoms), while MolProbity does not. MolProbity protonates the terminal hydroxyls on the 2 DNA chains, while WHATIF does not. All hydrogens added by MolProbity appeared to be in reasonable geometries, while some of those added by WHATIF were not.

MolProbity and WHATIF were tested in 2008. Jmol was tested in 2026.

==See Also==
*[[Hydrogen bonds]]
*[[Resolution]]
*[[Quality assessment for molecular models]]
*[[Water in macromolecular models]]

==Content Attribution==

Most of the original content in this article was adapted, with permission, from documentation written earlier by [[User:Eric Martz]], for several locations in [[Protein Explorer]]: [http://proteinexplorer.org/iv_water.htm Water], [http://proteinexplorer.org/help_hyd.htm Hydrogens in PDB files], and ''Hydrogen'' in the [http://proteinexplorer.org/igloss.htm Help/Index/Glossary].

Thanks to John Badger for key contributions.

==Notes & References==
<references />

[[Category:Topic Page]]

Hydrogen in macromolecular models

2026-08-01T18:08:37Z

Eric Martz:

[[Image:Protein Hydrogens in electron Density 1yk4 Y13.jpg|thumb|left|320px|Experimental difference density peaks for hydrogen atoms at 0.69A resolution: [[1yk4]] Tyr 13]]
Approximately 50% of the atoms in a protein are hydrogen. However, hydrogen atoms are absent from most molecular models. Most crystals do not have sufficient [[resolution]] (1.0 Ångstroms or better is needed) to determine the positions of hydrogen atoms directly. It is easy to add hydrogens to macromolecular models, but the results are only as good as the molecular models themselves.

==Absence of Hydrogen Atoms in Most Macromolecular Models==

Hydrogen atoms are absent from most molecular models in Proteopedia, which come mostly from the [[Protein Data Bank]]. 83% of models in the [[Protein Data Bank]] lack hydrogen atoms (in May, 2024). This is because most macromolecular crystals do not have sufficient [[resolution]] to determine the positions of hydrogen atoms. However it is easy to [[#Adding Hydrogens|add hydrogen atoms]], and in fact it is a good idea, because it [[#Model Validation??|helps to correct and validate]] the molecular model.

Although their positions are not well defined empirically in the electron density maps from typical macromolecular crystals, sometimes [[#Adding Hydrogens|hydrogens are added]] to X-ray crystallographic models before they are deposited in the Protein Data Bank. This is the choice of the authors of the [[PDB file]]. Hydrogens are usually present in PDB files resulting from [[NMR]] analysis, and usually present in [[theoretical models]].

==Approximately 50% of Protein Atoms, and approximately 35% of Nucleic Acid Atoms, are Hydrogen==

In proteins, the average number of hydrogens per non-hydrogen atom, weighted to take into account the frequencies of amino acids, is 1.01. Thus, hydrogens are ~50% of all atoms in protein. Nucleic acids have fewer, ~35%.

To '''determine the percentage of atoms that are hydrogen''' in a model in Proteopedia, click on the word ''Jmol'' in the lower right corner of the rotatable molecular scene, and then on ''Console''. In the lower box of the Console window that opens, enter "select hydrogen" and note the atom count in the report in the upper box. Then do the same for "select not hydrogen".

To '''visualize hydrogen atoms''', use the ''FirstGlance'' link in the ''Resources'' section beneath the molecular scene. Once the model is displayed in [[FirstGlance in Jmol]], click on ''Vines''. Change the background to black with the background toggle button. Now click on ''Vines''. In the help panel for ''Vines'', check ''More detail''. Hydrogen atoms are white. To hide and then show them, check ''Hide hydrogens'', then uncheck it.

<blockquote>
The value 1.01, for the average number of protein hydrogens per non-hydrogen protein atom, was calculated from the values for each amino acid, weighted by average frequencies of amino acids. The frequencies employed are based on 1,021 unrelated proteins of known sequence, tabulated on page 5 in Creighton (1993)<ref>"Proteins, Structures and Molecular Properties", Thomas E. Creighton, 2nd ed., 1993, W. H. Freeman and Co.</ref>.
</blockquote>

==Hydrogens Present in Macromolecular Models==

===Empirically-Positioned Hydrogens in High-Resolution Crystallographic Models===

High [[resolution]] protein crystallography (1.2 Ångstroms or better) can assign some hydrogen positions empirically from the electron density map, and very high resolution crystals (1.0 Ångstroms or better) can assign the positions of most hydrogens.

* '''Example:''' The X-ray model of a tyrosine kinase SH2 domain [[1lkk]] at 1.0 Angstrom resolution contains 901 hydrogens and 920 non-hydrogen protein atoms (ratio 0.98, 49%), so approximately all of the hydrogens actually present are assigned positions.

===Theoretically-Positioned Hydrogens in Average-Resolution Crystallographic Models===

As explained above, most macromolecular crystals do not provide high enough resolution to detect hydrogen positions empirically. The median [[resolution]] of models in the [[Protein Data Bank]] is 2.0 Å.

*'''Example: No hydrogens''': The X-ray model in PDB file [[1hho]] for oxyhemoglobin (2.1 A resolution) contains no hydrogens.

*'''Example: Some hydrogens from theory''': The X-ray file [[1lfa]] (1.8 A resolution; an integrin adhesion protein domain) contains 312 waters each with 2 hydrogens (so 624 water hydrogens), plus 639 protein hydrogens for 2,939 non-hydrogen protein atoms, which account for only about 22% (639/~2,939) of the hydrogens actually present in this protein. The protein hydrogens in the model are the polar hydrogens: one hydrogen on each main chain nitrogen (three hydrogens/amino terminal nitrogen), and hydrogens on sidechain oxygens or nitrogens in Ser, Thr, Tyr, Lys, Arg, His, Asn, and Gln. None of the hydrogens covalently bonded to carbons are present. The hydrogens which are present are required for the molecular dynamics stages of refinement of the X-ray model in the popular crystallographic refinement program X-PLOR; some authors strip them out before submitting a [[PDB file]] and others leave them in. The [[Protein Data Bank]] accepts X-ray models either way, according to the preference of the depositor.

*'''Example: All hydrogens from theory''': [[4gl2]], a 2013 [[X-ray crystallographic]] model of a protein-RNA complex, has all hydrogens, yet at its [[resolution]] of 3.56 Å, no hydrogens could have been resolved in the electron density map.

===Hydrogens in NMR Models===

[[NMR]] methods also determine some hydrogen positions. Typically all hydrogens are modeled in before the molecule is folded to fit the NMR interatomic distance restraints; hence, all hydrogens are usually present in NMR models submitted to the PDB.

*'''Example:''' The calmodulin ensemble of 25 [[NMR]] models [[1cfc]] contains 1096 protein hydrogens and 1166 non-hydrogen protein atoms per model (ratio 0.94, 48.5%), thereby assigning positions for approximately all of the hydrogens actually present.
*'''Example:''' The lac repressor:DNA complex ensemble of 3 [[NMR]] models [[1lcd]] contains 294 protein hydrogens and 1197 non-hydrogen protein atoms per model (ratio 0.25, 19.7%). Only the polar protein hydrogens are present in this model. There are 141 hydrogens in the DNA, and 1,335 non-hydrogen DNA atoms (9.6%). Only the Watson-Crick and terminal deoxyribose hydrogens are present. All 138 water molecules are modeled as H<sub>2</sub>O. Individual models contain 243, 235, and 233 hydrogens. (Author E.M. did not determine the basis for these differences.)

==Adding Hydrogens From Theory==

It is easy to add hydrogens to macromolecular models ([[PDB files]]) using the highly-reliable free servers listed below. Beware that the results are only as good as the molecular models themselves. Uncertainties in the positions of non-hydrogen atoms will, of course, produce inaccurate positions for hydrogen atoms. In fact, the quality of the molecular model can be judged in part from how well the hydrogens fit into the spaces between the non-hydrogen atoms. This degree of fit is quantitated in the ''overall clash score'' reported by the first method below, ''Molprobity''.

* Use the Richardson Lab's easy and very powerful [http://molprobity.biochem.duke.edu/ MolProbity: All-Atom Contact Analysis] server. Hydrogens are added to both protein and nucleic acids (but not to water), and you can save the resulting [[PDB file]]. This server has the advantage that you also get a powerful analysis of the quality of the model, including which Gln/Asn/His residues should have their sidechains flipped, an overall clash score, etc. You can save a model with the recommended sidechains flipped. Also you can visualize clashes anywhere in the model, including with the sidechains flipped or not flipped.

* Use the Vriend Lab's [https://swift.cmbi.umcn.nl/servers/html/index.html WHATIF WWW Interface]. Hydrogens are added to both protein and nucleic acids '''and also to water'''.
**Under Classes (at left) click "Hydrogen (bonds)".
**Select "Add protons to the structure".
**Enter your PDB ID or upload a coordinate file.
**After the results appear, click on the pdb link to receive the coordinate file containing added hydrogens.

[[PDB files]] that you save from either of these methods, can, for example, be uploaded for visualization in [[FirstGlance in Jmol]].

===Test Results===

[[1d66]] is an early (1992) modest resolution (2.7 Å) crystallographic model containing protein, DNA and 51 water oxygens. MolProbity reports its clashscore as 11.7, 65th percentile. The model deposited in the [[PDB]] contains no hydrogen atoms.

{| class="wikitable" style="text-align:right"
|+ Results for 1d66
! Program !! Protein Hydrogens !! Nucleic Hydrogens !! Water Hydrogens !! Total Hydrogens
|-
| MolProbity || 982 || 427 || 0 || 1,409
|-
| WHATIF || 1,000 || 423 || 102 || 1,525
|-
| Jmol || 990 || 427 || 0 || 1,417
|}
'''1d66:''' WHATIF protonates the sulfurs in 12 cysteines that are coordinating 4 cadmium ions, and the 2 N terminal nitrogens (6 H atoms), while MolProbity does not. MolProbity protonates the terminal hydroxyls on the 2 DNA chains, while WHATIF does not. All hydrogens added by MolProbity appeared to be in reasonable geometries, while some of those added by WHATIF were not.

MolProbity and WHATIF were tested in 2008. Jmol was tested in 2026.

==See Also==
*[[Hydrogen bonds]]
*[[Resolution]]
*[[Quality assessment for molecular models]]
*[[Water in macromolecular models]]

==Content Attribution==

Most of the original content in this article was adapted, with permission, from documentation written earlier by [[User:Eric Martz]], for several locations in [[Protein Explorer]]: [http://proteinexplorer.org/iv_water.htm Water], [http://proteinexplorer.org/help_hyd.htm Hydrogens in PDB files], and ''Hydrogen'' in the [http://proteinexplorer.org/igloss.htm Help/Index/Glossary].

Thanks to John Badger for key contributions.

==Notes & References==
<references />

[[Category:Topic Page]]

Hydrogen in macromolecular models

2026-08-01T18:07:12Z

Eric Martz:

[[Image:Protein Hydrogens in electron Density 1yk4 Y13.jpg|thumb|left|320px|Experimental difference density peaks for hydrogen atoms at 0.69A resolution: [[1yk4]] Tyr 13]]
Approximately 50% of the atoms in a protein are hydrogen. However, hydrogen atoms are absent from most molecular models. Most crystals do not have sufficient [[resolution]] (1.0 Ångstroms or better is needed) to determine the positions of hydrogen atoms directly. It is easy to add hydrogens to macromolecular models, but the results are only as good as the molecular models themselves.

==Absence of Hydrogen Atoms in Most Macromolecular Models==

Hydrogen atoms are absent from most molecular models in Proteopedia, which come mostly from the [[Protein Data Bank]]. 83% of models in the [[Protein Data Bank]] lack hydrogen atoms (in May, 2024). This is because most macromolecular crystals do not have sufficient [[resolution]] to determine the positions of hydrogen atoms. However it is easy to [[#Adding Hydrogens|add hydrogen atoms]], and in fact it is a good idea, because it [[#Model Validation??|helps to correct and validate]] the molecular model.

Although their positions are not well defined empirically in the electron density maps from typical macromolecular crystals, sometimes [[#Adding Hydrogens|hydrogens are added]] to X-ray crystallographic models before they are deposited in the Protein Data Bank. This is the choice of the authors of the [[PDB file]]. Hydrogens are usually present in PDB files resulting from [[NMR]] analysis, and usually present in [[theoretical models]].

==Approximately 50% of Protein Atoms, and approximately 35% of Nucleic Acid Atoms, are Hydrogen==

In proteins, the average number of hydrogens per non-hydrogen atom, weighted to take into account the frequencies of amino acids, is 1.01. Thus, hydrogens are ~50% of all atoms in protein. Nucleic acids have fewer, ~35%.

To '''determine the percentage of atoms that are hydrogen''' in a model in Proteopedia, click on the word ''Jmol'' in the lower right corner of the rotatable molecular scene, and then on ''Console''. In the lower box of the Console window that opens, enter "select hydrogen" and note the atom count in the report in the upper box. Then do the same for "select not hydrogen".

To '''visualize hydrogen atoms''', use the ''FirstGlance'' link in the ''Resources'' section beneath the molecular scene. Once the model is displayed in [[FirstGlance in Jmol]], click on ''Vines''. Change the background to black with the background toggle button. Now click on ''Vines''. In the help panel for ''Vines'', check ''More detail''. Hydrogen atoms are white. To hide and then show them, check ''Hide hydrogens'', then uncheck it.

<blockquote>
The value 1.01, for the average number of protein hydrogens per non-hydrogen protein atom, was calculated from the values for each amino acid, weighted by average frequencies of amino acids. The frequencies employed are based on 1,021 unrelated proteins of known sequence, tabulated on page 5 in Creighton (1993)<ref>"Proteins, Structures and Molecular Properties", Thomas E. Creighton, 2nd ed., 1993, W. H. Freeman and Co.</ref>.
</blockquote>

==Hydrogens Present in Macromolecular Models==

===Empirically-Positioned Hydrogens in High-Resolution Crystallographic Models===

High [[resolution]] protein crystallography (1.2 Ångstroms or better) can assign some hydrogen positions empirically from the electron density map, and very high resolution crystals (1.0 Ångstroms or better) can assign the positions of most hydrogens.

* '''Example:''' The X-ray model of a tyrosine kinase SH2 domain [[1lkk]] at 1.0 Angstrom resolution contains 901 hydrogens and 920 non-hydrogen protein atoms (ratio 0.98, 49%), so approximately all of the hydrogens actually present are assigned positions.

===Theoretically-Positioned Hydrogens in Average-Resolution Crystallographic Models===

As explained above, most macromolecular crystals do not provide high enough resolution to detect hydrogen positions empirically. The median [[resolution]] of models in the [[Protein Data Bank]] is 2.0 Å.

*'''Example: No hydrogens''': The X-ray model in PDB file [[1hho]] for oxyhemoglobin (2.1 A resolution) contains no hydrogens.

*'''Example: Some hydrogens from theory''': The X-ray file [[1lfa]] (1.8 A resolution; an integrin adhesion protein domain) contains 312 waters each with 2 hydrogens (so 624 water hydrogens), plus 639 protein hydrogens for 2,939 non-hydrogen protein atoms, which account for only about 22% (639/~2,939) of the hydrogens actually present in this protein. The protein hydrogens in the model are the polar hydrogens: one hydrogen on each main chain nitrogen (three hydrogens/amino terminal nitrogen), and hydrogens on sidechain oxygens or nitrogens in Ser, Thr, Tyr, Lys, Arg, His, Asn, and Gln. None of the hydrogens covalently bonded to carbons are present. The hydrogens which are present are required for the molecular dynamics stages of refinement of the X-ray model in the popular crystallographic refinement program X-PLOR; some authors strip them out before submitting a [[PDB file]] and others leave them in. The [[Protein Data Bank]] accepts X-ray models either way, according to the preference of the depositor.

*'''Example: All hydrogens from theory''': [[4gl2]], a 2013 [[X-ray crystallographic]] model of a protein-RNA complex, has all hydrogens, yet at its [[resolution]] of 3.56 Å, no hydrogens could have been resolved in the electron density map.

===Hydrogens in NMR Models===

[[NMR]] methods also determine some hydrogen positions. Typically all hydrogens are modeled in before the molecule is folded to fit the NMR interatomic distance restraints; hence, all hydrogens are usually present in NMR models submitted to the PDB.

*'''Example:''' The calmodulin ensemble of 25 [[NMR]] models [[1cfc]] contains 1096 protein hydrogens and 1166 non-hydrogen protein atoms per model (ratio 0.94, 48.5%), thereby assigning positions for approximately all of the hydrogens actually present.
*'''Example:''' The lac repressor:DNA complex ensemble of 3 [[NMR]] models [[1lcd]] contains 294 protein hydrogens and 1197 non-hydrogen protein atoms per model (ratio 0.25, 19.7%). Only the polar protein hydrogens are present in this model. There are 141 hydrogens in the DNA, and 1,335 non-hydrogen DNA atoms (9.6%). Only the Watson-Crick and terminal deoxyribose hydrogens are present. All 138 water molecules are modeled as H<sub>2</sub>O. Individual models contain 243, 235, and 233 hydrogens. (Author E.M. did not determine the basis for these differences.)

==Adding Hydrogens From Theory==

It is easy to add hydrogens to macromolecular models ([[PDB files]]) using the highly-reliable free servers listed below. Beware that the results are only as good as the molecular models themselves. Uncertainties in the positions of non-hydrogen atoms will, of course, produce inaccurate positions for hydrogen atoms. In fact, the quality of the molecular model can be judged in part from how well the hydrogens fit into the spaces between the non-hydrogen atoms. This degree of fit is quantitated in the ''overall clash score'' reported by the first method below, ''Molprobity''.

* Use the Richardson Lab's easy and very powerful [http://molprobity.biochem.duke.edu/ MolProbity: All-Atom Contact Analysis] server. Hydrogens are added to both protein and nucleic acids (but not to water), and you can save the resulting [[PDB file]]. This server has the advantage that you also get a powerful analysis of the quality of the model, including which Gln/Asn/His residues should have their sidechains flipped, an overall clash score, etc. You can save a model with the recommended sidechains flipped. Also you can visualize clashes anywhere in the model, including with the sidechains flipped or not flipped.

* Use the Vriend Lab's [https://swift.cmbi.umcn.nl/servers/html/index.html WHATIF WWW Interface]. Hydrogens are added to both protein and nucleic acids '''and also to water'''.
**Under Classes (at left) click "Hydrogen (bonds)".
**Select "Add protons to the structure".
**Enter your PDB ID or upload a coordinate file.
**After the results appear, click on the pdb link to receive the coordinate file containing added hydrogens.

[[PDB files]] that you save from either of these methods, can, for example, be uploaded for visualization in [[FirstGlance in Jmol]].

===Test Results===

[[1d66]] is an early (1992) modest resolution (2.7 Å) crystallographic model containing protein, DNA and 51 water oxygens. MolProbity reports its clashscore as 11.7, 65th percentile. The model deposited in the [[PDB]] contains no hydrogen atoms. The results from the above two servers:

{| class="wikitable" style="text-align:right"
|+ Results for 1d66
! Server !! Protein Hydrogens !! Nucleic Hydrogens !! Water Hydrogens !! Total Hydrogens
|-
| MolProbity || 982 || 427 || 0 || 1,409
|-
| WHATIF || 1,000 || 423 || 102 || 1,525
|-
| Jmol || 990 || 427 || 0 || 1,417
|}
'''1d66:''' WHATIF protonates the sulfurs in 12 cysteines that are coordinating 4 cadmium ions, and the 2 N terminal nitrogens (6 H atoms), while MolProbity does not. MolProbity protonates the terminal hydroxyls on the 2 DNA chains, while WHATIF does not. All hydrogens added by MolProbity appeared to be in reasonable geometries, while some of those added by WHATIF were not.

MolProbity and WHATIF were tested in 2008. Jmol was tested in 2026.

==See Also==
*[[Hydrogen bonds]]
*[[Resolution]]
*[[Quality assessment for molecular models]]
*[[Water in macromolecular models]]

==Content Attribution==

Most of the original content in this article was adapted, with permission, from documentation written earlier by [[User:Eric Martz]], for several locations in [[Protein Explorer]]: [http://proteinexplorer.org/iv_water.htm Water], [http://proteinexplorer.org/help_hyd.htm Hydrogens in PDB files], and ''Hydrogen'' in the [http://proteinexplorer.org/igloss.htm Help/Index/Glossary].

Thanks to John Badger for key contributions.

==Notes & References==
<references />

[[Category:Topic Page]]

Hydrogen in macromolecular models

2026-08-01T16:51:08Z

Eric Martz:

[[Image:Protein Hydrogens in electron Density 1yk4 Y13.jpg|thumb|left|320px|Experimental difference density peaks for hydrogen atoms at 0.69A resolution: [[1yk4]] Tyr 13]]
Approximately 50% of the atoms in a protein are hydrogen. However, hydrogen atoms are absent from most molecular models. Most crystals do not have sufficient [[resolution]] (1.0 Ångstroms or better is needed) to determine the positions of hydrogen atoms directly. It is easy to add hydrogens to macromolecular models, but the results are only as good as the molecular models themselves.

==Absence of Hydrogen Atoms in Most Macromolecular Models==

Hydrogen atoms are absent from most molecular models in Proteopedia, which come mostly from the [[Protein Data Bank]]. 83% of models in the [[Protein Data Bank]] lack hydrogen atoms (in May, 2024). This is because most macromolecular crystals do not have sufficient [[resolution]] to determine the positions of hydrogen atoms. However it is easy to [[#Adding Hydrogens|add hydrogen atoms]], and in fact it is a good idea, because it [[#Model Validation??|helps to correct and validate]] the molecular model.

Although their positions are not well defined empirically in the electron density maps from typical macromolecular crystals, sometimes [[#Adding Hydrogens|hydrogens are added]] to X-ray crystallographic models before they are deposited in the Protein Data Bank. This is the choice of the authors of the [[PDB file]]. Hydrogens are usually present in PDB files resulting from [[NMR]] analysis, and usually present in [[theoretical models]].

==Approximately 50% of Protein Atoms, and approximately 35% of Nucleic Acid Atoms, are Hydrogen==

In proteins, the average number of hydrogens per non-hydrogen atom, weighted to take into account the frequencies of amino acids, is 1.01. Thus, hydrogens are ~50% of all atoms in protein. Nucleic acids have fewer, ~35%.

To '''determine the percentage of atoms that are hydrogen''' in a model in Proteopedia, click on the word ''Jmol'' in the lower right corner of the rotatable molecular scene, and then on ''Console''. In the lower box of the Console window that opens, enter "select hydrogen" and note the atom count in the report in the upper box. Then do the same for "select not hydrogen".

To '''visualize hydrogen atoms''', use the ''FirstGlance'' link in the ''Resources'' section beneath the molecular scene. Once the model is displayed in [[FirstGlance in Jmol]], click on ''Vines''. Change the background to black with the background toggle button. Now click on ''Vines''. In the help panel for ''Vines'', check ''More detail''. Hydrogen atoms are white. To hide and then show them, check ''Hide hydrogens'', then uncheck it.

<blockquote>
The value 1.01, for the average number of protein hydrogens per non-hydrogen protein atom, was calculated from the values for each amino acid, weighted by average frequencies of amino acids. The frequencies employed are based on 1,021 unrelated proteins of known sequence, tabulated on page 5 in Creighton (1993)<ref>"Proteins, Structures and Molecular Properties", Thomas E. Creighton, 2nd ed., 1993, W. H. Freeman and Co.</ref>.
</blockquote>

==Hydrogens Present in Macromolecular Models==

===Empirically-Positioned Hydrogens in High-Resolution Crystallographic Models===

High [[resolution]] protein crystallography (1.2 Ångstroms or better) can assign some hydrogen positions empirically from the electron density map, and very high resolution crystals (1.0 Ångstroms or better) can assign the positions of most hydrogens.

* '''Example:''' The X-ray model of a tyrosine kinase SH2 domain [[1lkk]] at 1.0 Angstrom resolution contains 901 hydrogens and 920 non-hydrogen protein atoms (ratio 0.98, 49%), so approximately all of the hydrogens actually present are assigned positions.

===Theoretically-Positioned Hydrogens in Average-Resolution Crystallographic Models===

As explained above, most macromolecular crystals do not provide high enough resolution to detect hydrogen positions empirically. The median [[resolution]] of models in the [[Protein Data Bank]] is 2.0 Å.

*'''Example: No hydrogens''': The X-ray model in PDB file [[1hho]] for oxyhemoglobin (2.1 A resolution) contains no hydrogens.

*'''Example: Some hydrogens from theory''': The X-ray file [[1lfa]] (1.8 A resolution; an integrin adhesion protein domain) contains 312 waters each with 2 hydrogens (so 624 water hydrogens), plus 639 protein hydrogens for 2,939 non-hydrogen protein atoms, which account for only about 22% (639/~2,939) of the hydrogens actually present in this protein. The protein hydrogens in the model are the polar hydrogens: one hydrogen on each main chain nitrogen (three hydrogens/amino terminal nitrogen), and hydrogens on sidechain oxygens or nitrogens in Ser, Thr, Tyr, Lys, Arg, His, Asn, and Gln. None of the hydrogens covalently bonded to carbons are present. The hydrogens which are present are required for the molecular dynamics stages of refinement of the X-ray model in the popular crystallographic refinement program X-PLOR; some authors strip them out before submitting a [[PDB file]] and others leave them in. The [[Protein Data Bank]] accepts X-ray models either way, according to the preference of the depositor.

*'''Example: All hydrogens from theory''': [[4gl2]], a 2013 [[X-ray crystallographic]] model of a protein-RNA complex, has all hydrogens, yet at its [[resolution]] of 3.56 Å, no hydrogens could have been resolved in the electron density map.

===Hydrogens in NMR Models===

[[NMR]] methods also determine some hydrogen positions. Typically all hydrogens are modeled in before the molecule is folded to fit the NMR interatomic distance restraints; hence, all hydrogens are usually present in NMR models submitted to the PDB.

*'''Example:''' The calmodulin ensemble of 25 [[NMR]] models [[1cfc]] contains 1096 protein hydrogens and 1166 non-hydrogen protein atoms per model (ratio 0.94, 48.5%), thereby assigning positions for approximately all of the hydrogens actually present.
*'''Example:''' The lac repressor:DNA complex ensemble of 3 [[NMR]] models [[1lcd]] contains 294 protein hydrogens and 1197 non-hydrogen protein atoms per model (ratio 0.25, 19.7%). Only the polar protein hydrogens are present in this model. There are 141 hydrogens in the DNA, and 1,335 non-hydrogen DNA atoms (9.6%). Only the Watson-Crick and terminal deoxyribose hydrogens are present. All 138 water molecules are modeled as H<sub>2</sub>O. Individual models contain 243, 235, and 233 hydrogens. (Author E.M. did not determine the basis for these differences.)

==Adding Hydrogens From Theory==

It is easy to add hydrogens to macromolecular models ([[PDB files]]) using the highly-reliable free servers listed below. Beware that the results are only as good as the molecular models themselves. Uncertainties in the positions of non-hydrogen atoms will, of course, produce inaccurate positions for hydrogen atoms. In fact, the quality of the molecular model can be judged in part from how well the hydrogens fit into the spaces between the non-hydrogen atoms. This degree of fit is quantitated in the ''overall clash score'' reported by the first method below, ''Molprobity''.

* Use the Richardson Lab's easy and very powerful [http://molprobity.biochem.duke.edu/ MolProbity: All-Atom Contact Analysis] server. Hydrogens are added to both protein and nucleic acids (but not to water), and you can save the resulting [[PDB file]]. This server has the advantage that you also get a powerful analysis of the quality of the model, including which Gln/Asn/His residues should have their sidechains flipped, an overall clash score, etc. You can save a model with the recommended sidechains flipped. Also you can visualize clashes anywhere in the model, including with the sidechains flipped or not flipped.

* Use the Vriend Lab's [https://swift.cmbi.umcn.nl/servers/html/index.html WHATIF WWW Interface]. Hydrogens are added to both protein and nucleic acids '''and also to water'''.
**Under Classes (at left) click "Hydrogen (bonds)".
**Select "Add protons to the structure".
**Enter your PDB ID or upload a coordinate file.
**After the results appear, click on the pdb link to receive the coordinate file containing added hydrogens.

[[PDB files]] that you save from either of these methods, can, for example, be uploaded for visualization in [[FirstGlance in Jmol]].

[[1d66]] is an early (1992) modest resolution (2.7 Å) crystallographic model containing protein, DNA and 51 water oxygens. MolProbity reports its clashscore as 11.7, 65th percentile. The model deposited in the [[PDB]] contains no hydrogen atoms. The results from the above two servers:

{| class="wikitable" style="text-align:right"
|+ Comparing MolProbity and WHATIF on 1d66
! Server !! Protein Hydrogens !! Nucleic Hydrogens !! Water Hydrogens !! Total Hydrogens
|-
| MolProbity || 982 || 427 || 0 || 1,409
|-
| WHATIF || 1,000 || 423 || 102 || 1,525
|}
'''1d66:''' WHATIF protonates the sulfurs in 12 cysteines that are coordinating 4 cadmium ions, and the 2 N terminal nitrogens (6 H atoms), while MolProbity does not. MolProbity protonates the terminal hydroxyls on the 2 DNA chains, while WHATIF does not. All hydrogens added by MolProbity appeared to be in reasonable geometries, while some of those added by WHATIF were not.

==See Also==
*[[Hydrogen bonds]]
*[[Resolution]]
*[[Quality assessment for molecular models]]
*[[Water in macromolecular models]]

==Content Attribution==

Most of the original content in this article was adapted, with permission, from documentation written earlier by [[User:Eric Martz]], for several locations in [[Protein Explorer]]: [http://proteinexplorer.org/iv_water.htm Water], [http://proteinexplorer.org/help_hyd.htm Hydrogens in PDB files], and ''Hydrogen'' in the [http://proteinexplorer.org/igloss.htm Help/Index/Glossary].

Thanks to John Badger for key contributions.

==Notes & References==
<references />

[[Category:Topic Page]]

Protein Data Bank

2026-07-25T22:55:39Z

Eric Martz:

The [http://www.wwpdb.org World Wide Protein Data Bank] (wwPDB)<ref>PMID: 14634627</ref><ref>PMID: 17142228</ref> is the internationally recognized sole repository<ref>PMID: 30357364</ref> of all published, empirically-determined atomic resolution macromolecular three-dimensional (3D) structure data. Founded in 1971 by Drs. Edgar Meyer and Walter Hamilton at [http://www.bnl.gov Brookhaven National Laboratory]<REF>PMID:875032</REF><REF>PMID:10089483</REF>, management of the Protein Data Bank was headed by Tom Koestle until 1994 and then by [http://www.weizmann.ac.il/~joel Joel L. Sussman] till 1999, when it was transferred to members of the [http://home.rcsb.org/ Research Collaboratory for Structural Bioinformatics (RCSB)]. RCSB is managed at Rutgers University and the San Diego Supercomputer Center. It was directed by [http://en.wikipedia.org/wiki/Helen_M._Berman Helen M. Berman] until July 2014, when Stephen K. Burley took over the directorship<ref>[http://www.rcsb.org/pdb/general_information/news_publications/newsletters/2014q4/home.html#one2 Leadership Transition], RCSB Newsletter, Fall 2014.</ref>. In 2008, the PDB had three official branches: the Research Collaboratory for Structural Bioinformatics (RCSB, USA), the European Bioinformatics Institute (PDBe, UK), and the Protein Data Bank Japan (PDBj, Osaka). In 2022, Protein Data Bank China (PDBc, Shanghai) became an Associate Member.

==New Releases Cycle==
The wwPDB releases new entries once per week. These can be seen by clicking on the most recent release date, shown at the upper right of the main page at [http://pdb.org PDB.Org]. In 2007, 7,280 new entries were released (an average of 140/week). In 2011, 8,101 new entries were released (average 155/week).<ref>In May 2012, the following numbers were reported by advanced search on release dates at RCSB. 2011: 8,101. 2010: 7907. 2009: 7388. 2008: 6964. 2007: 7199.</ref>

While the traditional entry consisted of an [[Atomic coordinate file | atomic coordinate file]] molecular model, more recently, the '''experimental data''' (structure factors in the case of crystallography) have been deposited along with the the model. After February 1, 2008, deposition of experimental data is required along with all new entries.

Many derivative databases '''copy, derive information from, or add value to''' the [[Atomic coordinate file | atomic coordinate files]] available from the wwPDB. Often, these automatically update their databases weekly, shortly after the new releases become available at the PDB. Proteopedia is one example.

==PDB Statistics==
At [http://pdb.org pdb.org], at the upper right corner of the main page, click on ''PDB Statistics'' for a wealth of interesting information, including proteins solved by multiple experimental methods, sequence redundancy in the PDB, the distribution of [[Resolution|resolutions]], the 100 journals that have published the most new macromolecular structures, and graphs of the growth of the database (under ''Content Growth'').

Some interesting statistics (maxima, minima, means) for the contents of the PDB are summarized at [[Believe It or Not]].

==Remediation==

Periodically, the PDB remediates its archived data files. Remediation improves consistency and nomenclature and corrects some errors. Remediation involves changes in the [[Atomic_coordinate_file#PDB_Data_Format|PDB data format]]. Remediations occurred in August, 2007 and March, 2009. Details will be found at the [http://www.wwpdb.org/docs.html World Wide PDB].

Here are some examples of changes that occurred in remediations affecting the PDB format.
* '''DNA:''' Prior to August, 2007, both DNA and RNA nucleotides were named A, C, G, T, and U. After August, 2007, DNA nucleotides were changed to DA, DC, DG, DT and DU, while RNA nucleotides continued to use the older one-letter names. (An example of a model that contains both DNA and RNA is [[104d]].) This change required changes in software packages such as [[Jmol]], and left unmaintained packages such as [[Protein Explorer]] unable to deal properly with the remediated nucleic acids.
* '''Non-standard residues''': Some PDB files represented non-standard residues as a standard residue (ATOM records) plus an adduct (HETATM records). Some of these were changed to a uniform name for a non-standard residue, so that all atoms in the same residue have the same name (and all are HETATM records). For example, phosphoserine in [[1apm]] was SER plus PHO; phosphothreonine THR plus PHO. These were remediated to SEP and TPO. In another example, methylated ribonucleotides in [[310d]] had been named e.g. +C1 plus CH3. These were remediated to OMC and so forth.
* '''Order of atoms:''' In the March, 2009 remediation, the order of chains and atoms changed in some PDB files in a non-systematic manner. This broke some scenes that had been saved in Proteopedia, and required redesign of some portions of Proteopedia (see [[Getting_Unremediated_PDB_Files#Proteopedia avoids remediation-related problems|Proteopedia avoids remediation-related problems]]).

Obsolete (unremediated) versions of the data files were saved by the PDB before each remediation, and may be obtained: see [[Getting Unremediated PDB Files]].

==Sequence Numbering Anomalies==
Entries in the PDB often contain anomalies in sequence numbering (see [[Homology_modeling_servers#Sequence_Numbering_Anomalies]]).

==Improving Published Models==

There are several free automated servers that can improve most published models. See [[Improving published models]] and [[Quality assessment for molecular models]].

==More About The Protein Data Bank==

===See Also in Proteopedia===

*[[AlphaFold#AlphaFold_Database_of_Predictions|Database of structures predicted by AlphaFold2]].
*[[ModelArchive]] for [[Empirical models|non-empirical]] models.
*[[About Macromolecular Structure]], a list of pages in Proteopedia
*[[Atomic coordinate file]]
*[[Biological Unit]]
*[[PDB file]]
*[[PDB identification code]]
*[[Highest impact structures]] of all time
*[[Improving published models]]
*[[Quality assessment for molecular models]]

===External Sources===

*[http://www.wwpdb.org World Wide Protein Data Bank]
*[http://www.pdb.org RCSB PDB]
*[http://en.wikipedia.org/wiki/Protein_data_bank Protein Data Bank in Wikipedia]
*"Synergies between the Protein Data Bank and the community", 2021<ref name="synergies">PMID: 33963295</ref>.
*Berman H, Henrick K, Nakamura H, Markley JL. The worldwide Protein Data Bank (wwPDB): ensuring a single, uniform archive of PDB data. Nucleic Acids Res.35:D301-3. (2007) PMID:[http://www.ncbi.nlm.nih.gov/pubmed/17142228 17142228].
*Berman HM <i>et al.</i>, The Protein Data Bank, Acta Crystallogr D Biol Crystallogr.58:899-907 (2002). PMID:[http://www.ncbi.nlm.nih.gov/pubmed/12037327 12037327]
*H.M. Berman, J. Westbrook, Z. Feng, G. Gilliland, T.N. Bhat, H. Weissig, I.N. Shindyalov, P.E. Bourne: The Protein Data Bank. Nucleic Acids Research, 28 pp. 235-242 (2000). PMID:[http://www.ncbi.nlm.nih.gov/pubmed/10592235 10592235].
*Sussman JL, Lin D, Jiang J, Manning NO, Prilusky J, Ritter O, Abola EE (1998). "Protein data bank (PDB): a database of 3D structural information of biological macromolecules". ''Acta Cryst'' '''D54''':1078-1084. PMID 10089483.
*[http://www.umass.edu/microbio/rasmol/1st_xtls.htm Earliest Solutions for Macromolecular Crystal Structures]
*[https://www.rcsb.org/news/feature/66acd3c8eb1f4889a9e4432b 'PDB Archive Serves Structures Determined by Integrative and Hybrid Methods (IHM) (August 2024)']
*See also [[Proteopedia:Policy#Theoretical_Models | Theoretical Models]].

==References and Notes==
<references />

Protein Data Bank

2026-07-25T22:52:38Z

Eric Martz:

The [http://www.wwpdb.org World Wide Protein Data Bank] (wwPDB)<ref>PMID: 14634627</ref><ref>PMID: 17142228</ref> is the internationally recognized sole repository<ref>PMID: 30357364</ref> of all published, empirically-determined atomic resolution macromolecular three-dimensional (3D) structure data. Founded in 1971 by Drs. Edgar Meyer and Walter Hamilton at [http://www.bnl.gov Brookhaven National Laboratory]<REF>PMID:875032</REF><REF>PMID:10089483</REF>, management of the Protein Data Bank was headed by Tom Koestle until 1994 and then by [http://www.weizmann.ac.il/~joel Joel L. Sussman] till 1999, when it was transferred to members of the [http://home.rcsb.org/ Research Collaboratory for Structural Bioinformatics (RCSB)]. RCSB is managed at Rutgers University and the San Diego Supercomputer Center. It was directed by [http://en.wikipedia.org/wiki/Helen_M._Berman Helen M. Berman] until July 2014, when Stephen K. Burley took over the directorship<ref>[http://www.rcsb.org/pdb/general_information/news_publications/newsletters/2014q4/home.html#one2 Leadership Transition], RCSB Newsletter, Fall 2014.</ref>. In 2008, the PDB had three official branches: the Research Collaboratory for Structural Bioinformatics (RCSB, USA), the European Bioinformatics Institute (PDBe, UK), and the Protein Data Bank Japan (PDBj, Osaka). In 2022, Protein Data Bank China (PDBc) became an Associate Member.

==New Releases Cycle==
The wwPDB releases new entries once per week. These can be seen by clicking on the most recent release date, shown at the upper right of the main page at [http://pdb.org PDB.Org]. In 2007, 7,280 new entries were released (an average of 140/week). In 2011, 8,101 new entries were released (average 155/week).<ref>In May 2012, the following numbers were reported by advanced search on release dates at RCSB. 2011: 8,101. 2010: 7907. 2009: 7388. 2008: 6964. 2007: 7199.</ref>

While the traditional entry consisted of an [[Atomic coordinate file | atomic coordinate file]] molecular model, more recently, the '''experimental data''' (structure factors in the case of crystallography) have been deposited along with the the model. After February 1, 2008, deposition of experimental data is required along with all new entries.

Many derivative databases '''copy, derive information from, or add value to''' the [[Atomic coordinate file | atomic coordinate files]] available from the wwPDB. Often, these automatically update their databases weekly, shortly after the new releases become available at the PDB. Proteopedia is one example.

==PDB Statistics==
At [http://pdb.org pdb.org], at the upper right corner of the main page, click on ''PDB Statistics'' for a wealth of interesting information, including proteins solved by multiple experimental methods, sequence redundancy in the PDB, the distribution of [[Resolution|resolutions]], the 100 journals that have published the most new macromolecular structures, and graphs of the growth of the database (under ''Content Growth'').

Some interesting statistics (maxima, minima, means) for the contents of the PDB are summarized at [[Believe It or Not]].

==Remediation==

Periodically, the PDB remediates its archived data files. Remediation improves consistency and nomenclature and corrects some errors. Remediation involves changes in the [[Atomic_coordinate_file#PDB_Data_Format|PDB data format]]. Remediations occurred in August, 2007 and March, 2009. Details will be found at the [http://www.wwpdb.org/docs.html World Wide PDB].

Here are some examples of changes that occurred in remediations affecting the PDB format.
* '''DNA:''' Prior to August, 2007, both DNA and RNA nucleotides were named A, C, G, T, and U. After August, 2007, DNA nucleotides were changed to DA, DC, DG, DT and DU, while RNA nucleotides continued to use the older one-letter names. (An example of a model that contains both DNA and RNA is [[104d]].) This change required changes in software packages such as [[Jmol]], and left unmaintained packages such as [[Protein Explorer]] unable to deal properly with the remediated nucleic acids.
* '''Non-standard residues''': Some PDB files represented non-standard residues as a standard residue (ATOM records) plus an adduct (HETATM records). Some of these were changed to a uniform name for a non-standard residue, so that all atoms in the same residue have the same name (and all are HETATM records). For example, phosphoserine in [[1apm]] was SER plus PHO; phosphothreonine THR plus PHO. These were remediated to SEP and TPO. In another example, methylated ribonucleotides in [[310d]] had been named e.g. +C1 plus CH3. These were remediated to OMC and so forth.
* '''Order of atoms:''' In the March, 2009 remediation, the order of chains and atoms changed in some PDB files in a non-systematic manner. This broke some scenes that had been saved in Proteopedia, and required redesign of some portions of Proteopedia (see [[Getting_Unremediated_PDB_Files#Proteopedia avoids remediation-related problems|Proteopedia avoids remediation-related problems]]).

Obsolete (unremediated) versions of the data files were saved by the PDB before each remediation, and may be obtained: see [[Getting Unremediated PDB Files]].

==Sequence Numbering Anomalies==
Entries in the PDB often contain anomalies in sequence numbering (see [[Homology_modeling_servers#Sequence_Numbering_Anomalies]]).

==Improving Published Models==

There are several free automated servers that can improve most published models. See [[Improving published models]] and [[Quality assessment for molecular models]].

==More About The Protein Data Bank==

===See Also in Proteopedia===

*[[AlphaFold#AlphaFold_Database_of_Predictions|Database of structures predicted by AlphaFold2]].
*[[ModelArchive]] for [[Empirical models|non-empirical]] models.
*[[About Macromolecular Structure]], a list of pages in Proteopedia
*[[Atomic coordinate file]]
*[[Biological Unit]]
*[[PDB file]]
*[[PDB identification code]]
*[[Highest impact structures]] of all time
*[[Improving published models]]
*[[Quality assessment for molecular models]]

===External Sources===

*[http://www.wwpdb.org World Wide Protein Data Bank]
*[http://www.pdb.org RCSB PDB]
*[http://en.wikipedia.org/wiki/Protein_data_bank Protein Data Bank in Wikipedia]
*"Synergies between the Protein Data Bank and the community", 2021<ref name="synergies">PMID: 33963295</ref>.
*Berman H, Henrick K, Nakamura H, Markley JL. The worldwide Protein Data Bank (wwPDB): ensuring a single, uniform archive of PDB data. Nucleic Acids Res.35:D301-3. (2007) PMID:[http://www.ncbi.nlm.nih.gov/pubmed/17142228 17142228].
*Berman HM <i>et al.</i>, The Protein Data Bank, Acta Crystallogr D Biol Crystallogr.58:899-907 (2002). PMID:[http://www.ncbi.nlm.nih.gov/pubmed/12037327 12037327]
*H.M. Berman, J. Westbrook, Z. Feng, G. Gilliland, T.N. Bhat, H. Weissig, I.N. Shindyalov, P.E. Bourne: The Protein Data Bank. Nucleic Acids Research, 28 pp. 235-242 (2000). PMID:[http://www.ncbi.nlm.nih.gov/pubmed/10592235 10592235].
*Sussman JL, Lin D, Jiang J, Manning NO, Prilusky J, Ritter O, Abola EE (1998). "Protein data bank (PDB): a database of 3D structural information of biological macromolecules". ''Acta Cryst'' '''D54''':1078-1084. PMID 10089483.
*[http://www.umass.edu/microbio/rasmol/1st_xtls.htm Earliest Solutions for Macromolecular Crystal Structures]
*[https://www.rcsb.org/news/feature/66acd3c8eb1f4889a9e4432b 'PDB Archive Serves Structures Determined by Integrative and Hybrid Methods (IHM) (August 2024)']
*See also [[Proteopedia:Policy#Theoretical_Models | Theoretical Models]].

==References and Notes==
<references />

Converting AlphaFold3 CIF to PDB

2026-07-23T17:21:48Z

Eric Martz:

The [https://alphafoldserver.com AlphaFold3 Server] predicts models only in the [[Mmcif format|mmCIF format]] (filename ending '''.cif'''). These files<ref name="best">Each job produces 5 .cif files. The file with a name ending   _model_0.cif is one of those with the highest overall [https://alphafoldserver.com/faq pTM quality score]. The pTM quality score is in the corresponding '''_summary_confidences_0.json''' file. Open this file in a [[Help:Plain text editors|text editor]]. Look for the third-from-last line, which begins "ptm": (including the quotes) followed by the overall pTM confidence value. See the FAQ at the [https://alphafoldserver.com AlphaFold3 Server] for how to interpret pTM.</ref> can be visualized & analyzed using ''FirstGlance in Jmol '''version 4.6''''' available via '''[http://firstglance.jmol.org firstglance.jmol.org]''' (but not yet installed at proteopedia.org). These mmCIF files can also be uploaded to [[iCn3D]], or displayed in [[PyMOL]] or [[ChimeraX]].

Only [http://firstglance.jmol.org FirstGlance in Jmol] and [[iCn3D]] automatically color AlphaFold-predicted models by confidence/[[pLDDT]] correctly ('''{{Font color|blue|blue for high confidence}}, {{Font color|red|red for low confidence}}'''). See [[How_to_predict_structures_with_AlphaFold#Visualizing_Predicted_Structures|Visualizing Predicted Structures]].

FirstGlance also makes it [[FirstGlance/How to get average pLDDT from AlphaFold models|easy to get the average pLDDT]] for any range of residues that you specify.

The original version of this article discussed a method for converting AlphaFold 3 .cif models to .pdb format. ''''That is no longer necessary.'''' ''FirstGlance in Jmol '''version 4.6''''' accepts AlphaFold 3 .cif files directly via drag and drop.

About 5% of the models in the [[wwPDB]] are available only in mmCIF format ("CIF-only"). These are more complicated than AlphaFold models, and are not yet supported by FirstGlance. Support is expected later in 2026.

==Conversion Procedure==

You do not need this procedure to make AlphaFold Server .cif files compatible with FirstGlance in Jmol (see above). You can drop those .cif files directly into the [http://firstglance.jmol.org FrontDoor of FirstGlance].

The procedure below could be used, for example, to convert molecular models in XYZ format to PDB format. Most* CIF-only models from the [[wwPDB]] can also be converted (see ''Caution'' below).
<ol>
<li> Get the Jmol.jar Java application running on your computer by following the instructions at [[Jmol/Application]].
<li> Create a working folder (directory), and put Jmol.jar in it.
<li> Get the .cif file to convert. If you have downloaded a .cif file from the [[wwPDB]], you can skip the next 3 steps.
<ol type="a">
<li> Download the zip file from the [https://alphafoldserver.com AlphaFold3 Server].
<li> Double-click the zip file to unzip it.
<li> In the newly unzipped folder, find the file with a name ending '''_model_0.cif'''. Drag it into your working folder.<ref name="best">Each job produces 5 .cif files. The file with a name ending   _model_0.cif is one of those with the highest overall [https://alphafoldserver.com/faq pTM quality score]. The pTM quality score is in the corresponding '''_summary_confidences_0.json''' file. Open this file in a [[Help:Plain text editors|text editor]]. Look for the third-from-last line, which begins "ptm": (including the quotes) followed by the overall pTM confidence value. See the FAQ at the [https://alphafoldserver.com AlphaFold3 Server] for how to interpret pTM.</ref>
</ol>
<li> Double-click Jmol.jar to run it.
<li> Drag the .cif file and drop it into the black window of Jmol. The model should appear.
<li> In the white ''Jmol Script Console'', enter the command '''write jobname.pdb''', where ''jobname'' is a unique identifier for this model.
<li> Drag and drop ''jobname.pdb'' into [http://firstglance.jmol.org FirstGlance in Jmol].
</ol>

===Caution: Ligand Names May Be Wrong===

If your .cif file had 5-character ligand codes (instead of or in addition to 3-character ligand codes), conversion will truncate those 5-character codes to their first three characters.
(5-character ligand names were introduced after all 3-character codes were in use.)
For example, the ligand code [https://www.rcsb.org/ligand/A1EJM A1EJM] in [[9l63|9L63]] will be truncated to A1E in the converted PDB file. FirstGlance will handle it correctly except that under ''Ligands and Non-Standard Residues'' (in the Molecule Information Tab), '''the link (=?) will display the wrong chemical structure'''; namely, it will display ligand A1E instead of A1EJM.

To display the chemical structure of a ligand with a 5-character code, go to [http://rcsb.org RCSB.org] and enter the 5-character code into the search slot at the top, then press Enter.

To list all the ligand codes in your .cif file, after dropping the .cif file into the black window of Jmol.jar, enter these two '''bold commands''' in the white window (example is [[9dos]]):

<br>
<span style="color:magenta;">$</span> '''select hetero'''
<br>
94 atoms selected
<br>
<span style="color:magenta;">$</span> '''show residues'''
<br>
<span style="color:blue;">[GOL]501:A
<br>
[A1A8V]502:A
<br>
[A1A8V]501:B
<br>
[A1A8V]501:C
<br>
[A1A8V]501:D</span>

GOL is a 3-character ligand code (for glycerol), and A1A8V is a 5-character ligand code. "501:D" means residue number 501 in chain D.

==See Also==
*[[How to predict structures with AlphaFold]]
*[[AlphaFold/Index]]

==Notes==

<references />

Converting AlphaFold3 CIF to PDB

2026-07-23T17:19:47Z

Eric Martz:

The [https://alphafoldserver.com AlphaFold3 Server] predicts models only in the [[Mmcif format|mmCIF format]] (filename ending '''.cif'''). These files<ref name="best">Each job produces 5 .cif files. The file with a name ending   _model_0.cif is one of those with the highest overall [https://alphafoldserver.com/faq pTM quality score]. The pTM quality score is in the corresponding '''_summary_confidences_0.json''' file. Open this file in a [[Help:Plain text editors|text editor]]. Look for the third-from-last line, which begins "ptm": (including the quotes) followed by the overall pTM confidence value. See the FAQ at the [https://alphafoldserver.com AlphaFold3 Server] for how to interpret pTM.</ref> can be visualized & analyzed using ''FirstGlance in Jmol '''version 4.6''''' available via '''[http://firstglance.jmol.org firstglance.jmol.org]''' (but not yet installed at proteopedia.org). These mmCIF files can also be uploaded to [[iCn3D]], or displayed in [[PyMOL]] or [[ChimeraX]].

Only [http://firstglance.jmol.org FirstGlance in Jmol] and [[iCn3D]] automatically color AlphaFold-predicted models by confidence/[[pLDDT]] correctly ('''{{Font color|blue|blue for high confidence}}, {{Font color|red|red for low confidence}}'''). See [[How_to_predict_structures_with_AlphaFold#Visualizing_Predicted_Structures|Visualizing Predicted Structures]].

FirstGlance also makes it [[FirstGlance/How to get average pLDDT from AlphaFold models|easy to get the average pLDDT]] for any range of residues that you specify.

The original version of this article discussed a method for converting AlphaFold 3 .cif models to .pdb format. ''''That is no longer necessary.'''' ''FirstGlance in Jmol '''version 4.6''''' accepts AlphaFold 3 .cif files directly via drag and drop.

About 5% of the models in the [[wwPDB]] are available only in mmCIF format ("CIF-only"). These are more complicated than AlphaFold models, and are not yet supported by FirstGlance. Support is expected later in 2026.

==Conversion Procedure==

You do not need this procedure to make AlphaFold Server .cif files compatible with FirstGlance in Jmol (see above). You can drop those .cif files directly into the [http://firstglance.jmol.org FrontDoor of FirstGlance].

The procedure below could be used, for example, to convert molecular models in XYZ format to PDB format. Most* CIF-only models from the [[wwPDB]] can also be converted (see ''Caution'' below).
<ol>
<li> Get the Jmol.jar Java application running on your computer by following the instructions at [[Jmol/Application]].
<li> Create a working folder (directory), and put Jmol.jar in it.
<li> Get the .cif file to convert. If you have downloaded a .cif file from the [[wwPDB]], you can skip the next 3 steps.
<ol type="a">
<li> Download the zip file from the [https://alphafoldserver.com AlphaFold3 Server].
<li> Double-click the zip file to unzip it.
<li> In the newly unzipped folder, find the file with a name ending '''_model_0.cif'''. Drag it into your working folder.<ref name="best">Each job produces 5 .cif files. The file with a name ending   _model_0.cif is one of those with the highest overall [https://alphafoldserver.com/faq pTM quality score]. The pTM quality score is in the corresponding '''_summary_confidences_0.json''' file. Open this file in a [[Help:Plain text editors|text editor]]. Look for the third-from-last line, which begins "ptm": (including the quotes) followed by the overall pTM confidence value. See the FAQ at the [https://alphafoldserver.com AlphaFold3 Server] for how to interpret pTM.</ref>
</ol>
<li> Double-click Jmol.jar to run it.
<li> Drag the .cif file and drop it into the black window of Jmol. The model should appear.
<li> In the white ''Jmol Script Console'', enter the command '''write jobname.pdb''', where ''jobname'' is a unique identifier for this model.
<li> [http://firstglance.jmol.org/where.htm#uploading Upload] ''jobname.pdb'' to [http://firstglance.jmol.org FirstGlance in Jmol].
</ol>

===Caution: Ligand Names May Be Wrong===

If your .cif file had 5-character ligand codes (instead of or in addition to 3-character ligand codes), conversion will truncate those 5-character codes to their first three characters.
(5-character ligand names were introduced after all 3-character codes were in use.)
For example, the ligand code [https://www.rcsb.org/ligand/A1EJM A1EJM] in [[9l63|9L63]] will be truncated to A1E in the converted PDB file. FirstGlance will handle it correctly except that under ''Ligands and Non-Standard Residues'' (in the Molecule Information Tab), '''the link (=?) will display the wrong chemical structure'''; namely, it will display ligand A1E instead of A1EJM.

To display the chemical structure of a ligand with a 5-character code, go to [http://rcsb.org RCSB.org] and enter the 5-character code into the search slot at the top, then press Enter.

To list all the ligand codes in your .cif file, after dropping the .cif file into the black window of Jmol.jar, enter these two '''bold commands''' in the white window (example is [[9dos]]):

<br>
<span style="color:magenta;">$</span> '''select hetero'''
<br>
94 atoms selected
<br>
<span style="color:magenta;">$</span> '''show residues'''
<br>
<span style="color:blue;">[GOL]501:A
<br>
[A1A8V]502:A
<br>
[A1A8V]501:B
<br>
[A1A8V]501:C
<br>
[A1A8V]501:D</span>

GOL is a 3-character ligand code (for glycerol), and A1A8V is a 5-character ligand code. "501:D" means residue number 501 in chain D.

==See Also==
*[[How to predict structures with AlphaFold]]
*[[AlphaFold/Index]]

==Notes==

<references />

Converting AlphaFold3 CIF to PDB

2026-07-23T17:19:09Z

Eric Martz:

The [https://alphafoldserver.com AlphaFold3 Server] predicts models only in the [[Mmcif format|mmCIF format]] (filename ending '''.cif'''). These files<ref name="best">Each job produces 5 .cif files. The file with a name ending   _model_0.cif is one of those with the highest overall [https://alphafoldserver.com/faq pTM quality score]. The pTM quality score is in the corresponding '''_summary_confidences_0.json''' file. Open this file in a [[Help:Plain text editors|text editor]]. Look for the third-from-last line, which begins "ptm": (including the quotes) followed by the overall pTM confidence value. See the FAQ at the [https://alphafoldserver.com AlphaFold3 Server] for how to interpret pTM.</ref> can be visualized & analyzed using ''FirstGlance in Jmol '''version 4.6''''' available via '''[http://firstglance.jmol.org firstglance.jmol.org]''' (but not yet installed at proteopedia.org). These mmCIF files can also be uploaded to [[iCn3D]], or displayed in [[PyMOL]] or [[ChimeraX]].

Only [http://firstglance.jmol.org FirstGlance in Jmol] and [[iCn3D]] automatically color AlphaFold-predicted models by confidence/[[pLDDT]] correctly ('''{{Font color|blue|blue for high confidence}}, {{Font color|red|red for low confidence}}'''). See [[How_to_predict_structures_with_AlphaFold#Visualizing_Predicted_Structures|Visualizing Predicted Structures]].

FirstGlance also makes it [[FirstGlance/How to get average pLDDT from AlphaFold models|easy to get the average pLDDT]] for any range of residues that you specify.

The original version of this article discussed a method for converting AlphaFold 3 .cif models to .pdb format. ''''That is no longer necessary.'''' ''FirstGlance in Jmol '''version 4.6''''' accepts AlphaFold 3 .cif files directly via drag and drop.

About 5% of the models in the [[wwPDB]] are available only in mmCIF format ("CIF-only"). These are more complicated than AlphaFold models, and are not yet supported by FirstGlance. Support is expected later in 2026.



==See Also==
*[[How to predict structures with AlphaFold]]
*[[AlphaFold/Index]]

==Notes==

<references />

Converting AlphaFold3 CIF to PDB

2026-07-23T17:15:53Z

Eric Martz:

The [https://alphafoldserver.com AlphaFold3 Server] predicts models only in the [[Mmcif format|mmCIF format]] (filename ending '''.cif'''). These files<ref name="best">Each job produces 5 .cif files. The file with a name ending   _model_0.cif is one of those with the highest overall [https://alphafoldserver.com/faq pTM quality score]. The pTM quality score is in the corresponding '''_summary_confidences_0.json''' file. Open this file in a [[Help:Plain text editors|text editor]]. Look for the third-from-last line, which begins "ptm": (including the quotes) followed by the overall pTM confidence value. See the FAQ at the [https://alphafoldserver.com AlphaFold3 Server] for how to interpret pTM.</ref> can be visualized & analyzed using ''FirstGlance in Jmol '''version 4.6''''' available via '''[http://firstglance.jmol.org firstglance.jmol.org]''' (but not yet installed at proteopedia.org). These mmCIF files can also be uploaded to [[iCn3D]], or displayed in [[PyMOL]] or [[ChimeraX]].

Only [http://firstglance.jmol.org FirstGlance in Jmol] and [[iCn3D]] automatically color AlphaFold-predicted models by confidence/[[pLDDT]] correctly ('''{{Font color|blue|blue for high confidence}}, {{Font color|red|red for low confidence}}'''). See [[How_to_predict_structures_with_AlphaFold#Visualizing_Predicted_Structures|Visualizing Predicted Structures]].

FirstGlance also makes it [[FirstGlance/How to get average pLDDT from AlphaFold models|easy to get the average pLDDT]] for any range of residues that you specify.

The original version of this article discussed a method for converting AlphaFold 3 .cif models to .pdb format. ''''That is no longer necessary.'''' ''FirstGlance in Jmol '''version 4.6''''' accepts AlphaFold 3 .cif files directly via drag and drop.

About 5% of the models in the [[wwPDB]] are available only in mmCIF format ("CIF-only"). These are more complicated than AlphaFold models, and are not yet supported by FirstGlance. Support is expected later in 2026.



==See Also==
*[[How to predict structures with AlphaFold]]
*[[AlphaFold/Index]]

==Notes==

<references />

FirstGlance in Jmol Literature Citations

2026-07-17T19:59:23Z

Eric Martz:

The following publications in the scientific literature cite use of ''[[FirstGlance in Jmol]]''. This list excludes publications co-authored by [[User:Eric Martz]], the author of ''FirstGlance in Jmol''. (Those are listed at [https://scholar.google.com/citations?user=Bb3H0OsAAAAJ&hl=en&oi=ao Google Scholar: Eric Martz].) The 120 citations listed below in more than 30 [[#Journals Cited|peer-reviewed journals]] were found by searching full text using [https://scholar.google.com Google Scholar] (see [[#Coverage|Coverage]]), and all were verified to cite ''FirstGlance in Jmol''.
<table align="right" class="wikitable" width="500"><tr><td>
[[FirstGlance in Jmol]] offers, since 2006, free visualization and analysis of protein molecules and other macromolecules (DNA, RNA, oligosaccharides, etc.). It is easy to use and provides built-in guidance and help. In 2024, it was used on average '''265 times/day'''. For more, see
* [[FirstGlance in Jmol]]
* [http://firstglance.jmol.org/whatis.htm#unique Unique Capabilities of FirstGlance in Jmol]
* [https://www.youtube.com/@ericmartz9100 FirstGlance YouTube Channel] [[Image:Youtube.png]]
* [[FirstGlance/Index]], a list of resources about FirstGlance in Jmol, including all the relevant pages in Proteopedia.
* [http://firstglance.jmol.org Start FirstGlance in Jmol]
</td></tr></table>
Researchers took advantage of [http://firstglance.jmol.org/whatis.htm#unique unique capabilities] of ''FirstGlance'':
<ul>
<li>Visual analysis of structures predicted by '''AlphaFold2''', colored by '''reliability''' estimates.
<li>Calculation of average '''pLDDT''' for structures predicted by '''AlphaFold3'''.
<li>Seeing locations of [[Missing residues and incomplete sidechains|'''missing''' residues]], which affect shape, distribution of polar/hydrophobic surfaces, and may result in missing [[salt bridges]] and [[cation-pi interactions]].
<li>Locating '''mutations''' in the 3D model.
<li>Positions of proteins in lipid bilayer '''membranes''' (models from [https://opm.phar.umich.edu/ OPM U. Mich.]).
<li>Coloring amino acids by evolutionary '''conservation''' (determined by [https://consurf.tau.ac.il ConSurf]) to identify functional sites.
<li>Rejection of models with '''Rfree''' below average for their resolutions.
<li>Applying sequence '''numbering''' to the 3D view.
<li>Seeing the distribution of hydrophobic vs. '''polar''' amino acids.
<li>Percentages of '''secondary''' structure elements.
<li>Locating residues or regions of interest, using ''Find'' to apply yellow '''halos'''.
<li>Distribution and counts of '''charged''' residues.
<li>Visual '''isolation''' of domains or regions of interest.
<li>Identification of '''contact residues'''.
</ul>
<span style="background-color:#fffce0;">Use your browser's ''Find in page'' (Control-f / Command-f) to locate studies involving the '''bold''' terms above. Some of these capabilities are illustrated with animations generated by ''FirstGlance'' at [https://tinyurl.com/movingmolecules tinyurl.com/movingmolecules].</span>
__NOTOC__

==2026==

==={{Font color|#ff8000|Education & Communication}}===

<ref group="xtra">PMID: 41854287</ref><references group="xtra" />

==={{Font color|#00b000|BioMedical Research}}===

<ref group="xtra">PMID: 42375539</ref><references group="xtra" />

<ref group="xtra">PMID: 42395897</ref><references group="xtra" />

<ref group="xtra">PMID: 42344113</ref><references group="xtra" />

<ref group="xtra">PMID: 41504448</ref><references group="xtra" />

==2021-2025==

==={{Font color|#ff8000|Education & Communication}}===

<ref group="xtra">PMID: 39976303</ref><references group="xtra" />

* [https://www.google.com/books/edition/Food_Chemistry_in_Small_Bites/QLk_EQAAQBAJ O'Hara, Patricia B. Food Chemistry in Small Bites: The Alchemist in the Kitchen. Univ of California Press; 2025 Apr 15.]

<ref group="xtra">PMID: 39291955</ref><references group="xtra" />

<ref group="xtra">PMID: 35001912</ref><references group="xtra" />

==={{Font color|#00b000|BioMedical Research}}===
====2025====
<ref group="xtra">PMID: 41390121</ref><references group="xtra" />

<ref group="xtra">PMID: 41060696</ref><references group="xtra" />
<blockquote><span style="background-color:#fffce0;">
For AlphaFold3-predicted structures, "Average '''pLDDT''' scores were calculated using FirstGlance in Jmol."
</span>
</blockquote>

<ref group="xtra">PMID: 41331102</ref><references group="xtra" />

<ref group="xtra">PMID: 41047069</ref><references group="xtra" />

<ref group="xtra">PMID: 41072766</ref><references group="xtra" />

<table align="right"><tr><td>
[[Image:Sefid-consurf-teplizumab-2025.png]]
</td><td width="250">
Figure 2 from Sefid ''et al.'', 2025.
'''Conservation''' of amino acids in Teplizumab analyzed using the ConSurf Server and displayed by FirstGlance in Jmol.
Reproduced in accord with the Creative Commons Attribution Deed<ref name="cca4i" />
</td></tr></table>
* [https://d1wqtxts1xzle7.cloudfront.net/123175184/4_DR_sefid-libre.pdf Sefid F, Monshizadeh K, Ghenaatzadeh R, Roodgarpour Z, Azamirad G, Mirhosseini H. Antibody Engineering Toward Enhancement of Teplizumab Anti-CD3 Binding Affinity in Type 1 Diabetes Prevention and Treatment. Iranian Journal of Diabetes and Obesity. 2025 May 10;17(2):97-109.]

<table align="right"><tr><td>
[[Image:Garcia-e-lyta-fig5-microorgs2025.png|300px]]
</td><td width="250">
Figure 5 from García, 2025. Molecular rendering of [[4x36]] by FirstGlance in Jmol. Reproduced with written permission from Ernesto Garcia (April 29, 2025).
</td></tr></table>
<ref group="xtra">PMID: 40284663</ref><references group="xtra" />

<ref group="xtra">PMID: 39299531</ref><references group="xtra" />

* [https://www.biorxiv.org/content/10.1101/2025.04.11.648320v1.full Weber H, Ehinger A, Kolb D, Fallahzadeh-Mamaghani V, Halter T, Franz-Wachtel M, zur Oven-Krockhaus S, Gronnier J, Zipfel C, Harter K, Kemmerling B. Arabidopsis HYPERSENSITIVE INDUCED REACTION 2 affects plasma membrane receptor pathways and organization. bioRxiv. 2025:2025-04.]
<blockquote>
<span style="background-color:#fffce0;">"AlphaFold2 modeling of HIR2 and analysis of the '''distribution of polar amino acids by FirstGlance''' revealed an N-terminal surface-exposed platform of HIR2 that consists of nonpolar residues, which could interact with hydrophobic parts of the (plasma) membrane."</span>
</blockquote>

<ref group="xtra">PMID: 39758030</ref><references group="xtra" />

====2024====
<table align="right"><tr><td>
[[Image:Martinez-alcantar-2024-fig1-1ol5.png|500px]]
</td><td width="250">
Fig. 1, [[1ol5]], from Martinez ''et al.'', 2024. Molecular rendering and Å scale by FirstGlance in Jmol; black labels added by Martinez ''et al.''.
Reproduced in accord with the Creative Commons Attribution Deed<ref name="cca4i">This work was published under the [https://creativecommons.org/licenses/by/4.0/ Creative Commons Attribution 4.0 International Deed].</ref>.
</td></tr></table>

<ref group="xtra">PMID: 39636801</ref><references group="xtra" />
<blockquote>
<span style="background-color:#fffce0;">FirstGlance in Jmol was used to visualize and tabulate '''missing residues''' in [[2az5]].</span>
(See [[Missing residues and incomplete sidechains]].)
</blockquote>

* [https://publish.kne-publishing.com/index.php/IJDO/article/view/15710 Sefid, Fateme, et al. "Antibody Engineering to Enhancement of Ranibizumab Binding Affinity for the Prevention and Treatment of Diabetic Retinopathy." Iranian journal of diabetes and obesity (2024).]

<ref group="xtra">PMID: 37904054</ref><references group="xtra" />

* [https://www.mdpi.com/2813-3757/2/4/23 Martínez-Alcantar, Lorena, et al. "Cyclic Peptides as Protein Kinase Modulators and Their Involvement in the Treatment of Diverse Human Diseases." Kinases and Phosphatases 2.4 (2024): 346-378.]

<ref group="xtra">PMID: 38968704</ref><references group="xtra" />
<blockquote>
<span style="background-color:#fffce0;">FirstGlance was used to visualize models predicted by '''AlphaFold2, colored by reliablity scores'''.</span>
</blockquote>

<table align="right"><tr><td>
[[Image:Gajta et al 2024 Fig3C Isolated domain from AlphaFold2.png|400px]]
</td><td width="250">
Fig. 3C, and AlphaFold2 prediction, from Gajda ''et al.'', 2024. Isolation of this domain, sequence numbering (applied with a single checkbox), and molecular rendering by FirstGlance in Jmol.
Reproduced in accord with the Creative Commons Attribution Deed<ref name="cca4i" />.
</td></tr></table>

<ref group="xtra">PMID: 38731903</ref><references group="xtra" />

<ref group="xtra">PMID: 39052973</ref><references group="xtra" />
<blockquote>
<span style="background-color:#fffce0;">'''Transmembrane secondary structure segments''' were evaluated using FirstGlance prior to docking analysis.</span>
</blockquote>

* [https://onlinelibrary.wiley.com/doi/full/10.1155/2024/1575103 Pan Y, Yao X, Yang TN, Li JL, Shi DF. The VP1/2 Protein of a New Recombinant PRV Strain Promotes the Infectivity and Pathogenicity of PRV in Northeastern China. Transboundary and Emerging Diseases. 2024;2024(1):1575103.]
<blockquote>
<span style="background-color:#fffce0;">FirstGlance was used to '''locate mutations''' in the 3D structure.</span>
</blockquote>

====2023====

<ref group="xtra">PMID: 37154976</ref><references group="xtra" />

<ref group="xtra">PMID: 37464933</ref><references group="xtra" />

* [https://www.biorxiv.org/content/10.1101/2023.05.28.542320.abstract Sondhi Y, Messcher RL, Bellantuano AJ, Storer CG, Cinel SD, Godfrey RK, Glass D, St Laurent RA, Hamilton CA, Earl C, Brislawn CJ. The developmental gene disco regulates diel-niche evolution in adult moths. bioRxiv. 2023 May 28:2023-05.]

* [https://dc.etsu.edu/context/etd/article/5760/viewcontent/PremaA052323f.pdf Prema A. Mapping The Binding Site Within Integrin αD β2 for Carboxyethylpyrrole (CEP)-Modified Proteins (2023). Electronic Theses and Dissertations, East Tennessee State University. Paper 4232.]

* [https://link.springer.com/article/10.1007/s11816-022-00788-4 Hassan MM, Martin S, Feng K, Yates TB, Yuan G, Martin MZ, Martin S, Muchero W, Griffiths NA, Weston DJ, Yang X. Genome-wide identification and functional prediction of silicon (Si) transporters in poplar (Populus trichocarpa). Plant Biotechnology Reports. 2023 Apr;17(2):285-302.]

<ref group="xtra">PMID: 36670408</ref><references group="xtra" />

====2022====
<table align="right"><tr><td>
[[Image:Puccio-2021-mol-micro.png|300px]]
</td><td width="250">
Graphical Abstract from Puccio ''et al.'', 2022. Molecular rendering by FirstGlance in Jmol. <font color="red">'''Red'''</font> and <font color="blue">'''Blue'''</font> planes represent boundaries of the lipid bilayer membrane. Reproduced in accord with the Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International
Deed<ref name="ccannd4i">This work was published under the [https://creativecommons.org/licenses/by-nc-nd/4.0/ Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International Deed].</ref>.
</td></tr></table>
<ref group="xtra">PMID: 34855265</ref><references group="xtra" />
<blockquote>
<span style="background-color:#fffce0;">"'''Positions within a cellular membrane''' were predicted using OPM (https://opm.phar.umich.edu/) and visualized in JMol 3.0 using FirstGlance."</span>
</blockquote>

<ref group="xtra">PMID: 35869579</ref><references group="xtra" />

<ref group="xtra">PMID: 36120551</ref><references group="xtra" />

<ref group="xtra">PMID: 35537348</ref><references group="xtra" />

<table align="right"><tr><td>
[[Image:Camelo, lopez-pazos 2022 fig 7-CClic.png|400px]]
</td><td width="250">
Figure 5 from Camelo ''et al.'', 2025. Molecular rendering by FirstGlance in Jmol. Reproduced in accord with the Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International
Deed<ref name="ccansa4i">This work was published under the [https://creativecommons.org/licenses/by-nc-sa/4.0/deed.en Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International Deed].</ref>.
</td></tr></table>
* [http://scielo.senescyt.gob.ec/scielo.php?pid=S1390-85962022000200032&script=sci_abstract&tlng=en Lozano Camelo OC, Rojas Arias AC, Ávila Méndez KJ, López-Pazos SA. Preservación modificada y descripción de la fungalisina para Batrachochytrium dendrobatidis. LA GRANJA. Revista de Ciencias de la Vida. 2022 Feb;36(2):32-44.]

<ref group="xtra">PMID: 35493110</ref><references group="xtra" />

<ref group="xtra">PMID: 35742992</ref><references group="xtra" />

* [https://dl.acm.org/doi/abs/10.1145/3570773.3570833 Xu Y. The Analysis of Tiotropium bromide and Roflumilast: Two Potent Medications for Chronic Obstructive Pulmonary Disease. InProceedings of the 3rd International Symposium on Artificial Intelligence for Medicine Sciences 2022 Oct 13 (pp. 231-238).]

<ref group="xtra">PMID: 35228627</ref><references group="xtra" />

<ref group="xtra">PMID: 35139120</ref><references group="xtra" />

====2021====

<ref group="xtra">PMID: 34619810</ref><references group="xtra" />

<ref group="xtra">PMID: 32496928</ref><references group="xtra" />

<ref group="xtra">PMID: 34786595</ref><references group="xtra" />

* [https://www.frontiersin.org/articles/10.3389/fevo.2021.666564/full Junker N, Gossmann TI. Adaptation-driven evolution of sirtuin 1 (SIRT1), a key regulator of metabolism and aging, in marmot species. Frontiers in Ecology and Evolution. 2021 Jul 2;9:666564.]

* [http://jommid.pasteur.ac.ir/browse.php?a_id=345&sid=1&slc_lang=en&ftxt=0 Sefid F, Khalesi B, Mansoori B, Fotovvat M, Touhidinia M. Enhancement of SARS-CoV-2 Receptor Binding Domain-CR3022 Human Antibody Binding Affinity via In silico Engineering Approach. Journal of Medical Microbiology and Infectious Diseases. 2021 Sep 10;9(3):156-69.]

* [https://link.springer.com/article/10.1007/s10725-021-00735-3 Brunoni F, Rolli E, Polverini E, Spíchal L, Ricci A. The adjuvant activity of two urea derivatives on cytokinins: An example of serendipitous dual effect. Plant Growth Regulation. 2021 Nov;95:169-90.]

==2016-2020==

==={{Font color|#ff8000|Education & Communication}}===

<ref group="xtra">PMID: 32077575</ref><references group="xtra" />
<blockquote>
<span style="background-color:#fffce0;">Lee ''et al.'', 2020, said "... browser-based applications or interfaces (e.g., ''FirstGlance in Jmol'') increase accessibility for students. Hands-on use of visualization software by students seems to benefit their 3D understanding of proteins better than simply viewing it on-screen."</span>
</blockquote>

* [https://pubs.acs.org/doi/10.1021/acs.jchemed.8b00426 Cation−Π Interactions in Biochemistry: A Primer, Miguel O. Mitchell and John Means, J. Chem. Educ. 2018, 95, 12, 2284–2288.]

<ref group="xtra">PMID: 28214437</ref><references group="xtra" />

==={{Font color|#00b000|BioMedical Research}}===
====2020====
<table align="right"><tr><td>
[[Image:Lin et al 2020 Fig2d 1hk0.png|300px]]
</td><td width="250">
Fig. 2d from Lin ''et al.'', 2020. '''Secondary structure percentages''' and molecular rendering by ''FirstGlance in Jmol''.
Reproduced in accord with the Creative Commons Attribution-NonCommercial 4.0 International
Deed<ref name="ccanc4i">This work was published under the [https://creativecommons.org/licenses/by-nc/4.0/ Creative Commons Attribution-NonCommercial 4.0 International Deed].</ref>.
</td></tr></table>
<ref group="xtra">PMID: 33460241</ref><references group="xtra" />

<ref group="xtra">PMID: 31702846</ref><references group="xtra" />
<blockquote>
<span style="background-color:#fffce0;">Ben Chorin ''et al.'', 2020, wrote "The '''conservation grades (colors) are mapped onto the three-dimensional structure of the query protein''', which can be viewed using ... FirstGlance in Jmol. This visualization is highly enlightening because it emphasizes the important, evolutionarily conserved regions of the protein."</span>
</blockquote>

<ref group="xtra">PMID: 31608807</ref><references group="xtra" />

<table align="right"><tr><td>
[[Image:McGurk et la 2020 Fig 2I,J tankyrase-binding domain halos 4bs2.png|500px]]
</td><td width="250">
Portions of Fig. 2I,J from McGurk ''et al.'', 2020. The '''tankyrase-binding-domain of [[4bs2]] was identified ({{Yelspan|yellow halos}}) with the ''Find'' tool''' of ''FirstGlance in Jmol''. ''FirstGlance'' also added the sequence labels.
Reproduced in accord with the Creative Commons Attribution 4.0 International
Deed<ref name="cca4i" />.
</td></tr></table>
<ref group="xtra">PMID: 32409565</ref><references group="xtra" />

<ref group="xtra">PMID: 32531564</ref><references group="xtra" />

<ref group="xtra">PMID: 32706779</ref><references group="xtra" />
<blockquote>
<span style="background-color:#fffce0;">Shalit and Tuvi-Arad, 2020, wrote "For each protein [565 were analyzed], we calculated the Rfree grade as defined by FirstGlance in Jmol .... '''Files were kept if their Rfree grade was at least "average" at their resolution.'''"</span>
</blockquote>

<ref group="xtra">PMID: 32123543</ref><references group="xtra" />
<blockquote>
<span style="background-color:#fffce0;">Mattila ''et al.'' 2020 provided a downloadable PDB file with a link to view it by uploading to ''FirstGlance in Jmol''.</span>
</blockquote>

<ref group="xtra">PMID: 32867961</ref><references group="xtra" />

* [http://op.niscpr.res.in/index.php/IJBB/article/viewFile/29116/465477657 Zaheer ZA, Sankaranarayanan K. In silico analysis of κ-theraphotoxin-Cg2a from Chilobrachys guangxiensis. Indian Journal of Biochemistry and Biophysics (IJBB). 2020 Jul 28;57(4):458-66.]

====2019====
<ref group="xtra">PMID: 31058389</ref><references group="xtra" />

<ref group="xtra">PMID: 31172379</ref><references group="xtra" />

<ref group="xtra">PMID: 31018129</ref><references group="xtra" />

<ref group="xtra">PMID: 30791384</ref><references group="xtra" />

====2018====
<ref group="xtra">PMID: 30346734</ref><references group="xtra" />

<ref group="xtra">PMID: 29534001</ref><references group="xtra" />

<ref group="xtra">PMID: 29567208</ref><references group="xtra" />

<ref group="xtra">PMID: 30398106</ref><references group="xtra" />

<ref group="xtra">PMID: 29684709</ref><references group="xtra" />

<ref group="xtra">PMID: 29704154</ref><references group="xtra" />

<ref group="xtra">PMID: 30381731</ref><references group="xtra" />

* [https://link.springer.com/article/10.1134/S1068162018020024 Podlesnykh SV, Shanshin DV, Kolosova EA, Murashkin DE, Shaprova ON, Shcherbakov DN, Chapoval AI. Development of Search Strategy for Peptide Inhibitors of Immune Checkpoints. Russian Journal of Bioorganic Chemistry. 2018 Mar;44:150-7.]

====2017====

<ref group="xtra">PMID: 29262419</ref><references group="xtra" />

<ref group="xtra">PMID: 28791129</ref><references group="xtra" />

<ref group="xtra">PMID: 29079705</ref><references group="xtra" />

<ref group="xtra">PMID: 28302399</ref><references group="xtra" />

<ref group="xtra">PMID: 28872841</ref><references group="xtra" />

<ref group="xtra">PMID: 28434129</ref><references group="xtra" />

<ref group="xtra">PMID: 30258911</ref><references group="xtra" />

====2016====

* [https://www.researchgate.net/profile/Rahul-Shelake/publication/309241483_Structural_Analysis_and_Homology_Modeling_of_Members_of_smt-like_Operon_from_Thermophilic_Cyanobacterium_Thermosynechococcus_elongatus_BP-1/links/58099b9708ae1c98c25263e3/Structural-Analysis-and-Homology-Modeling-of-Members-of-smt-like-Operon-from-Thermophilic-Cyanobacterium-Thermosynechococcus-elongatus-BP-1.pdf Shelake RM, Hayashi H, Morita EH. Structural analysis and homology modeling of members of smt-like operon from thermophilic cyanobacterium Thermosynechococcus elongatus BP-1. J Proteins Proteomics. 2016;7(3):221-30.]

<ref group="xtra">PMID: 27400707</ref><references group="xtra" />

<ref group="xtra">PMID: 26866676</ref><references group="xtra" />
<blockquote>
<span style="background-color:#fffce0;">See Figure 2 which uses ''FirstGlance in Jmol'' to '''highlight critical lysine residues''' in nucleosome histones with yellow halos. That Figure is not reproduced here because ACS denies permission to non-profit organizations, unless payment is made.</span>
</blockquote>

<ref group="xtra">PMID: 26043781</ref><references group="xtra" />
<blockquote>
<span style="background-color:#fffce0;">''FirstGlance in Jmol'' was used to '''locate and count charged residues'''.</span>
</blockquote>

<ref group="xtra">PMID: 27347491</ref><references group="xtra" />

* [https://www.academia.edu/download/79451787/medicinalchemistry-2-1016.pdf Santiago-Ruiz S, Polverini E, Manjarrez J, Espinoza KA, Reynoso E, Rivero IA. Virtual Screening of Putative Anticonvulsant Hydantoin Derived Drugs and Biological Evaluation. Ann. Med. Chem. Res. 2016;2(1):1016-23.]

<ref group="xtra">PMID: 26608339</ref><references group="xtra" />

==2011-2015==

===Coverage===
<table style="background-color:#ffe0e0;"><tr><td>
Coverage is nearly complete for the most recent decade 2016-2025 (above), as far as publications found with the methods used<ref name="gsmethods">In scholar.google.com, the query ''firstglance'' finds mostly irrelevant papers with the term ''first glance''. Quoting the query, ''"firstglance"'' was used to restrict hits to that exact single word. However, some papers erroneously cite ''First Glance in Jmol'', or even say something like ''Jmol, with the First Glance''. Therefore, a second search was done using ''"first glance" and jmol''.</ref> in [https://scholar.google.com Google Scholar]. For years before 2016 (below), only an arbitrary subset of citations is listed.
</td></tr></table>

==={{Font color|#ff8000|Education & Communication}}===

<ref group="xtra">PMID: 24591499</ref><references group="xtra" />
<blockquote>
<span style="background-color:#fffce0;">Barber & Stark wrote "FirstGlance in Jmol is a simple platform with sophisticated functionality for viewing a molecule's structure with different diagrams, cross-sections, and emphasis on various molecular features."</span>
</blockquote>

<ref group="xtra">PMID: 24979189</ref><references group="xtra" />

<ref group="xtra">PMID: 23649886</ref><references group="xtra" />

* [https://onlinelibrary.wiley.com/doi/abs/10.1002/ijch.201300024 Hanson RM, Prilusky J, Renjian Z, Nakane T, Sussman JL. JSmol and the next‐generation web‐based representation of 3D molecular structure as applied to proteopedia. Israel Journal of Chemistry. 2013 Apr;53(3‐4):207-16.]

<ref group="xtra">PMID: 23354749</ref><references group="xtra" />
<blockquote>
<span style="background-color:#fffce0;">Forest writes "Structures should be made to come alive in articles. ... [A] straightforward option is to include a link to the NSF-supported Java-based application ''Firstglance in Jmol'' that will allow the reader to call up the pdb file in a simple Web-based viewer that is browser independent."</span>
</blockquote>

<ref group="xtra">PMID: 24019219</ref><references group="xtra" />
<blockquote>
<span style="background-color:#fffce0;">Figure 1 is an excellent example of how a student used ''FirstGlance in Jmol'' to '''visualize hydrophobic cores'''. That Figure is not reproduced here because obtaining permission from Wiley Publications is complicated and may require payment even for a non-profit educational organization with open access on the Internet.</span>
</blockquote>

<ref group="xtra">PMID: 23166023</ref><references group="xtra" />
<blockquote>
<span style="background-color:#fffce0;">''FirstGlance in Jmol'' was the sole 3D visualization tool provided to students in this study.</span>
</blockquote>

* [https://pubs.acs.org/doi/full/10.1021/ed101022g Saderholm, Matthew, and Anthony Reynolds. "Jmol-enhanced biochemistry research projects." Journal of Chemical Education 88.8 (2011): 1074-1078.].

==={{Font color|#00b000|BioMedical Research}}===
<span style="background-color:#ffe0e0;">[[#Coverage|Partial Coverage]]</span>

<ref group="xtra">PMID: 25785714</ref><references group="xtra" />

<ref group="xtra">PMID: 26224535</ref><references group="xtra" />

<table align="right"><tr><td>
[[Image:Chen et al 2012 Fig 1 3g04.png|500px]]
</td><td width="250">
Fig. 1 from Chen ''et al.'', 2012. Atomic rendering of the leucine-rich repeat domain of the thyroid-stimulating hormone receptor by ''FirstGlance in Jmol'' showing hydrophobic vs. polar regions and charge distribution.
Yellow halos highlight charged residues at the C-terminal "base" of the domain.
Reproduced in accord with the Creative Commons Attribution 4.0 International
Deed<ref name="cca4i" />.
</td></tr></table>

<ref group="xtra">PMID: 25336027</ref><references group="xtra" />

<ref group="xtra">PMID: 24692644</ref><references group="xtra" />

* [https://pubs.acs.org/doi/abs/10.1021/bk-2013-1142.ch016 Fleming SA. Teaching tools for organic and bio-organic chemistry. In Pedagogic Roles of Animations and Simulations in Chemistry Courses 2013 (pp. 389-409). American Chemical Society.]

<ref group="xtra">PMID: 22359649</ref><references group="xtra" />

<ref group="xtra">PMID: 22235356</ref><references group="xtra" />

<ref group="xtra">PMID: 23119066</ref><references group="xtra" />

<ref group="xtra">PMID: 22069494</ref><references group="xtra" />

<ref group="xtra">PMID: 21472436</ref><references group="xtra" />
<blockquote>
<span style="background-color:#fffce0;">In 2011, the '''Protein Structure Initiative's''' Structural Biology '''Knowledgebase''' offers ''FirstGlance in Jmol'' as a structure viewer.</span>
</blockquote>

<ref group="xtra">PMID: 22440564</ref><references group="xtra" />

==2006-2010==

==={{Font color|#ff8000|Education & Communication}}===
<span style="background-color:#ffe0e0;">[[#Coverage|Partial Coverage]]</span>

<ref group="xtra">PMID: 21567875</ref><references group="xtra" />
<blockquote>
<span style="background-color:#fffce0;">... applications such as the excellent, FirstGlance in Jmol provide a quick and simple way to view and manipulate structures ....</span>
</blockquote>

<ref group="xtra">PMID: 20504857</ref><references group="xtra" />
<blockquote>
<span style="background-color:#fffce0;">Porollo and Meller wrote "Protein–ligand contacts are determined using the respective procedure adopted in Protein Explorer and subsequently in the FirstGlance in Jmol server (FGiJ) that accounts for hydrogen bonds, water and salt bridges, hydrophobic and aromatic ring interaction and different types of metals binding. For the corresponding bond distance definitions, the reader is referred to the FGiJ documentation." '''This excellent server continues to be available in 2025''' as [https://polyview.cchmc.org/polyview3d.html PolyView-3D], and is linked at the Martz website [http://molviz.org MolviZ.Org].</span>
</blockquote>

<ref group="xtra">PMID: 20541422</ref><references group="xtra" />

<ref group="xtra">PMID: 20195256</ref><references group="xtra" />

<ref group="xtra">PMID: 21567685</ref><references group="xtra" />
<blockquote>
<span style="background-color:#fffce0;">''FirstGlance in Jmol'' was the primary visualization package provided to students in this curriculum.</span>
</blockquote>

<ref group="xtra">PMID: 19230677</ref><references group="xtra" />
<blockquote>
<span style="background-color:#fffce0;">Hodis and Sussman wrote "... widely available
molecular visualization programs ... are
often inaccessible to non-specialists owing to a steep learning curve (with, in our opinion, FirstGlance in Jmol being an exception)."</span>
</blockquote>

<ref group="xtra">PMID: 19847312</ref><references group="xtra" />

* [https://pmc.ncbi.nlm.nih.gov/articles/PMC2762578/ Palmer III AG, Matthews BW. Interactive graphics return to protein science. Protein Science: A Publication of the Protein Society. 2009 Mar 20;18(4):677.]

<ref group="xtra">PMID: 19461848</ref><references group="xtra" />
<blockquote>
<span style="background-color:#fffce0;">Interactivity allows a reader unbounded scope to explore a structure, taking advantage of whatever features the visualization software may provide. This is the basis underlying FirstGlance in Jmol, a service that an increasing number of journals link to, which provides standard buttons to view different aspects of a protein structure ....</span>
</blockquote>

<ref group="xtra">PMID: 21638687</ref><references group="xtra" />
<blockquote>
<span style="background-color:#fffce0;">Herráez said "I express my gratitude to Prof. Eric Martz (University of Massachusetts), long-time advocate of molecular modeling teaching, provider of Rasmol and Chime information and support on his website, of teaching-oriented recommendations and sample materials, of the excellent Protein Explorer software for macromolecule visualization and analysis, and of other countless contributions, including the recent FirstGlance in Jmol."</span>
</blockquote>

==={{Font color|#00b000|BioMedical Research}}===
<span style="background-color:#ffe0e0;">[[#Coverage|Partial Coverage]]</span>

<ref group="xtra">PMID: 20634950</ref><references group="xtra" />
<blockquote>
<span style="background-color:#fffce0;">''FirstGlance in Jmol'' was used to visualize patterns of '''evolutionary conservation''' calculated by the [http://consurf.tau.ac.il ConSurf Server].</span>
</blockquote>

<ref group="xtra">PMID: 21029378</ref><references group="xtra" />

<ref group="xtra">PMID: 18971256</ref><references group="xtra" />

<ref group="xtra">PMID: 19329630</ref><references group="xtra" />

<ref group="xtra">PMID: 19233205</ref><references group="xtra" />

* [https://books.google.com/books?hl=en&lr=&id=3jq1kSKcvEAC&oi=fnd&pg=PR11&dq=firstglance&ots=XchA-jpK7C&sig=TKhk00SK4YHR3QtLqXZU23d0jK8 Courey AJ. Mechanisms in transcriptional regulation. John Wiley & Sons; 2009 Jan 22.]
<blockquote>
<span style="background-color:#fffce0;">"''FirstGlance in Jmol'': This free program, also developed by Eric Martz, is probably '''the easiest way to look at macromolecules'''."</span>
</blockquote>

<ref group="xtra">PMID: 18067320</ref><references group="xtra" />
<blockquote>
<span style="background-color:#fffce0;">"The "'''contact residues'''" of the SH3 domain with the ligand were assigned by means of the FirstGlance in Jmol program ...."</span>
</blockquote>

<ref group="xtra">PMID: 19081051</ref><references group="xtra" />

<ref group="xtra">PMID: 18347046</ref><references group="xtra" />

==Journals Cited==

Peer-reviewed scientific papers listed above that cite ''FirstGlance in Jmol'' were published in numerous journals, including
===Education Journals===
''Biochemistry and Molecular Biology Education (8), Journal of Chemical Education.''

===Basic Research Journals===
''ACS Chemical Biology, Archives of Biophysics & Biochemistry, Biochemistry (3), BMC Microbiology, Cell Reports, Current Opinion in Virology, European Journal of Cell Biology, FEBS Journal, Gene, Journal of Cell Science, Journal of Bacteriology (2), Journal of Biological Chemistry, Journal of Molecular Biology, Molecular Microbiology, Nature Methods, Nucleic Acids Research (2), Planta, Plant Growth Regulation, Plant Cell Reports, PLOS One (9), Protein Science (3), Structure*, Scientific Reports, Trends in Biochemical Sciences (2), Veterinary Journal''.

<nowiki>*</nowiki> Nimrod ''et al.'', 2008.

===Medical Journals===
''Annals of Neurology, Infection & Immunity, Leukemia, Medical Microbiology & Immunology, PLOS Neglected Tropical Diseases.''

==References==
<references />

FirstGlance in Jmol Literature Citations

2026-07-17T19:52:46Z

Eric Martz:

The following publications in the scientific literature cite use of ''[[FirstGlance in Jmol]]''. This list excludes publications co-authored by [[User:Eric Martz]], the author of ''FirstGlance in Jmol''. (Those are listed at [https://scholar.google.com/citations?user=Bb3H0OsAAAAJ&hl=en&oi=ao Google Scholar: Eric Martz].) The 120 citations listed below in more than 30 [[#Journals Cited|peer-reviewed journals]] were found by searching full text using [https://scholar.google.com Google Scholar] (see [[#Coverage|Coverage]]), and all were verified to cite ''FirstGlance in Jmol''.
<table align="right" class="wikitable" width="500"><tr><td>
[[FirstGlance in Jmol]] offers, since 2006, free visualization and analysis of protein molecules and other macromolecules (DNA, RNA, oligosaccharides, etc.). It is easy to use and provides built-in guidance and help. In 2024, it was used on average '''265 times/day'''. For more, see
* [[FirstGlance in Jmol]]
* [http://firstglance.jmol.org/whatis.htm#unique Unique Capabilities of FirstGlance in Jmol]
* [https://www.youtube.com/@ericmartz9100 FirstGlance YouTube Channel] [[Image:Youtube.png]]
* [[FirstGlance/Index]], a list of resources about FirstGlance in Jmol, including all the relevant pages in Proteopedia.
* [http://firstglance.jmol.org Start FirstGlance in Jmol]
</td></tr></table>
Researchers took advantage of [http://firstglance.jmol.org/whatis.htm#unique unique capabilities] of ''FirstGlance'':
<ul>
<li>Visual analysis of structures predicted by '''AlphaFold2''', colored by '''reliability''' estimates.
<li>Calculation of average '''pLDDT''' for structures predicted by '''AlphaFold3'''.
<li>Seeing locations of [[Missing residues and incomplete sidechains|'''missing''' residues]], which affect shape, distribution of polar/hydrophobic surfaces, and may result in missing [[salt bridges]] and [[cation-pi interactions]].
<li>Locating '''mutations''' in the 3D model.
<li>Positions of proteins in lipid bilayer '''membranes''' (models from [https://opm.phar.umich.edu/ OPM U. Mich.]).
<li>Coloring amino acids by evolutionary '''conservation''' (determined by [https://consurf.tau.ac.il ConSurf]) to identify functional sites.
<li>Rejection of models with '''Rfree''' below average for their resolutions.
<li>Applying sequence '''numbering''' to the 3D view.
<li>Seeing the distribution of hydrophobic vs. '''polar''' amino acids.
<li>Percentages of '''secondary''' structure elements.
<li>Locating residues or regions of interest, using ''Find'' to apply yellow '''halos'''.
<li>Distribution and counts of '''charged''' residues.
<li>Visual '''isolation''' of domains or regions of interest.
<li>Identification of '''contact residues'''.
</ul>
<span style="background-color:#fffce0;">Use your browser's ''Find in page'' (Control-f / Command-f) to locate studies involving the '''bold''' terms above. Some of these capabilities are illustrated with animations generated by ''FirstGlance'' at [https://tinyurl.com/movingmolecules tinyurl.com/movingmolecules].</span>
__NOTOC__

==2026==

==={{Font color|#ff8000|Education & Communication}}===

<ref group="xtra">PMID: 41854287</ref><references group="xtra" />

==={{Font color|#00b000|BioMedical Research}}===

<ref group="xtra">PMID: 42395897</ref><references group="xtra" />

<ref group="xtra">PMID: 42344113</ref><references group="xtra" />

<ref group="xtra">PMID: 41504448</ref><references group="xtra" />

==2021-2025==

==={{Font color|#ff8000|Education & Communication}}===

<ref group="xtra">PMID: 39976303</ref><references group="xtra" />

* [https://www.google.com/books/edition/Food_Chemistry_in_Small_Bites/QLk_EQAAQBAJ O'Hara, Patricia B. Food Chemistry in Small Bites: The Alchemist in the Kitchen. Univ of California Press; 2025 Apr 15.]

<ref group="xtra">PMID: 39291955</ref><references group="xtra" />

<ref group="xtra">PMID: 35001912</ref><references group="xtra" />

==={{Font color|#00b000|BioMedical Research}}===
====2025====
<ref group="xtra">PMID: 41390121</ref><references group="xtra" />

<ref group="xtra">PMID: 41060696</ref><references group="xtra" />
<blockquote><span style="background-color:#fffce0;">
For AlphaFold3-predicted structures, "Average '''pLDDT''' scores were calculated using FirstGlance in Jmol."
</span>
</blockquote>

<ref group="xtra">PMID: 41331102</ref><references group="xtra" />

<ref group="xtra">PMID: 41047069</ref><references group="xtra" />

<ref group="xtra">PMID: 41072766</ref><references group="xtra" />

<table align="right"><tr><td>
[[Image:Sefid-consurf-teplizumab-2025.png]]
</td><td width="250">
Figure 2 from Sefid ''et al.'', 2025.
'''Conservation''' of amino acids in Teplizumab analyzed using the ConSurf Server and displayed by FirstGlance in Jmol.
Reproduced in accord with the Creative Commons Attribution Deed<ref name="cca4i" />
</td></tr></table>
* [https://d1wqtxts1xzle7.cloudfront.net/123175184/4_DR_sefid-libre.pdf Sefid F, Monshizadeh K, Ghenaatzadeh R, Roodgarpour Z, Azamirad G, Mirhosseini H. Antibody Engineering Toward Enhancement of Teplizumab Anti-CD3 Binding Affinity in Type 1 Diabetes Prevention and Treatment. Iranian Journal of Diabetes and Obesity. 2025 May 10;17(2):97-109.]

<table align="right"><tr><td>
[[Image:Garcia-e-lyta-fig5-microorgs2025.png|300px]]
</td><td width="250">
Figure 5 from García, 2025. Molecular rendering of [[4x36]] by FirstGlance in Jmol. Reproduced with written permission from Ernesto Garcia (April 29, 2025).
</td></tr></table>
<ref group="xtra">PMID: 40284663</ref><references group="xtra" />

<ref group="xtra">PMID: 39299531</ref><references group="xtra" />

* [https://www.biorxiv.org/content/10.1101/2025.04.11.648320v1.full Weber H, Ehinger A, Kolb D, Fallahzadeh-Mamaghani V, Halter T, Franz-Wachtel M, zur Oven-Krockhaus S, Gronnier J, Zipfel C, Harter K, Kemmerling B. Arabidopsis HYPERSENSITIVE INDUCED REACTION 2 affects plasma membrane receptor pathways and organization. bioRxiv. 2025:2025-04.]
<blockquote>
<span style="background-color:#fffce0;">"AlphaFold2 modeling of HIR2 and analysis of the '''distribution of polar amino acids by FirstGlance''' revealed an N-terminal surface-exposed platform of HIR2 that consists of nonpolar residues, which could interact with hydrophobic parts of the (plasma) membrane."</span>
</blockquote>

<ref group="xtra">PMID: 39758030</ref><references group="xtra" />

====2024====
<table align="right"><tr><td>
[[Image:Martinez-alcantar-2024-fig1-1ol5.png|500px]]
</td><td width="250">
Fig. 1, [[1ol5]], from Martinez ''et al.'', 2024. Molecular rendering and Å scale by FirstGlance in Jmol; black labels added by Martinez ''et al.''.
Reproduced in accord with the Creative Commons Attribution Deed<ref name="cca4i">This work was published under the [https://creativecommons.org/licenses/by/4.0/ Creative Commons Attribution 4.0 International Deed].</ref>.
</td></tr></table>

<ref group="xtra">PMID: 39636801</ref><references group="xtra" />
<blockquote>
<span style="background-color:#fffce0;">FirstGlance in Jmol was used to visualize and tabulate '''missing residues''' in [[2az5]].</span>
(See [[Missing residues and incomplete sidechains]].)
</blockquote>

* [https://publish.kne-publishing.com/index.php/IJDO/article/view/15710 Sefid, Fateme, et al. "Antibody Engineering to Enhancement of Ranibizumab Binding Affinity for the Prevention and Treatment of Diabetic Retinopathy." Iranian journal of diabetes and obesity (2024).]

<ref group="xtra">PMID: 37904054</ref><references group="xtra" />

* [https://www.mdpi.com/2813-3757/2/4/23 Martínez-Alcantar, Lorena, et al. "Cyclic Peptides as Protein Kinase Modulators and Their Involvement in the Treatment of Diverse Human Diseases." Kinases and Phosphatases 2.4 (2024): 346-378.]

<ref group="xtra">PMID: 38968704</ref><references group="xtra" />
<blockquote>
<span style="background-color:#fffce0;">FirstGlance was used to visualize models predicted by '''AlphaFold2, colored by reliablity scores'''.</span>
</blockquote>

<table align="right"><tr><td>
[[Image:Gajta et al 2024 Fig3C Isolated domain from AlphaFold2.png|400px]]
</td><td width="250">
Fig. 3C, and AlphaFold2 prediction, from Gajda ''et al.'', 2024. Isolation of this domain, sequence numbering (applied with a single checkbox), and molecular rendering by FirstGlance in Jmol.
Reproduced in accord with the Creative Commons Attribution Deed<ref name="cca4i" />.
</td></tr></table>

<ref group="xtra">PMID: 38731903</ref><references group="xtra" />

<ref group="xtra">PMID: 39052973</ref><references group="xtra" />
<blockquote>
<span style="background-color:#fffce0;">'''Transmembrane secondary structure segments''' were evaluated using FirstGlance prior to docking analysis.</span>
</blockquote>

* [https://onlinelibrary.wiley.com/doi/full/10.1155/2024/1575103 Pan Y, Yao X, Yang TN, Li JL, Shi DF. The VP1/2 Protein of a New Recombinant PRV Strain Promotes the Infectivity and Pathogenicity of PRV in Northeastern China. Transboundary and Emerging Diseases. 2024;2024(1):1575103.]
<blockquote>
<span style="background-color:#fffce0;">FirstGlance was used to '''locate mutations''' in the 3D structure.</span>
</blockquote>

====2023====

<ref group="xtra">PMID: 37154976</ref><references group="xtra" />

<ref group="xtra">PMID: 37464933</ref><references group="xtra" />

* [https://www.biorxiv.org/content/10.1101/2023.05.28.542320.abstract Sondhi Y, Messcher RL, Bellantuano AJ, Storer CG, Cinel SD, Godfrey RK, Glass D, St Laurent RA, Hamilton CA, Earl C, Brislawn CJ. The developmental gene disco regulates diel-niche evolution in adult moths. bioRxiv. 2023 May 28:2023-05.]

* [https://dc.etsu.edu/context/etd/article/5760/viewcontent/PremaA052323f.pdf Prema A. Mapping The Binding Site Within Integrin αD β2 for Carboxyethylpyrrole (CEP)-Modified Proteins (2023). Electronic Theses and Dissertations, East Tennessee State University. Paper 4232.]

* [https://link.springer.com/article/10.1007/s11816-022-00788-4 Hassan MM, Martin S, Feng K, Yates TB, Yuan G, Martin MZ, Martin S, Muchero W, Griffiths NA, Weston DJ, Yang X. Genome-wide identification and functional prediction of silicon (Si) transporters in poplar (Populus trichocarpa). Plant Biotechnology Reports. 2023 Apr;17(2):285-302.]

<ref group="xtra">PMID: 36670408</ref><references group="xtra" />

====2022====
<table align="right"><tr><td>
[[Image:Puccio-2021-mol-micro.png|300px]]
</td><td width="250">
Graphical Abstract from Puccio ''et al.'', 2022. Molecular rendering by FirstGlance in Jmol. <font color="red">'''Red'''</font> and <font color="blue">'''Blue'''</font> planes represent boundaries of the lipid bilayer membrane. Reproduced in accord with the Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International
Deed<ref name="ccannd4i">This work was published under the [https://creativecommons.org/licenses/by-nc-nd/4.0/ Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International Deed].</ref>.
</td></tr></table>
<ref group="xtra">PMID: 34855265</ref><references group="xtra" />
<blockquote>
<span style="background-color:#fffce0;">"'''Positions within a cellular membrane''' were predicted using OPM (https://opm.phar.umich.edu/) and visualized in JMol 3.0 using FirstGlance."</span>
</blockquote>

<ref group="xtra">PMID: 35869579</ref><references group="xtra" />

<ref group="xtra">PMID: 36120551</ref><references group="xtra" />

<ref group="xtra">PMID: 35537348</ref><references group="xtra" />

<table align="right"><tr><td>
[[Image:Camelo, lopez-pazos 2022 fig 7-CClic.png|400px]]
</td><td width="250">
Figure 5 from Camelo ''et al.'', 2025. Molecular rendering by FirstGlance in Jmol. Reproduced in accord with the Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International
Deed<ref name="ccansa4i">This work was published under the [https://creativecommons.org/licenses/by-nc-sa/4.0/deed.en Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International Deed].</ref>.
</td></tr></table>
* [http://scielo.senescyt.gob.ec/scielo.php?pid=S1390-85962022000200032&script=sci_abstract&tlng=en Lozano Camelo OC, Rojas Arias AC, Ávila Méndez KJ, López-Pazos SA. Preservación modificada y descripción de la fungalisina para Batrachochytrium dendrobatidis. LA GRANJA. Revista de Ciencias de la Vida. 2022 Feb;36(2):32-44.]

<ref group="xtra">PMID: 35493110</ref><references group="xtra" />

<ref group="xtra">PMID: 35742992</ref><references group="xtra" />

* [https://dl.acm.org/doi/abs/10.1145/3570773.3570833 Xu Y. The Analysis of Tiotropium bromide and Roflumilast: Two Potent Medications for Chronic Obstructive Pulmonary Disease. InProceedings of the 3rd International Symposium on Artificial Intelligence for Medicine Sciences 2022 Oct 13 (pp. 231-238).]

<ref group="xtra">PMID: 35228627</ref><references group="xtra" />

<ref group="xtra">PMID: 35139120</ref><references group="xtra" />

====2021====

<ref group="xtra">PMID: 34619810</ref><references group="xtra" />

<ref group="xtra">PMID: 32496928</ref><references group="xtra" />

<ref group="xtra">PMID: 34786595</ref><references group="xtra" />

* [https://www.frontiersin.org/articles/10.3389/fevo.2021.666564/full Junker N, Gossmann TI. Adaptation-driven evolution of sirtuin 1 (SIRT1), a key regulator of metabolism and aging, in marmot species. Frontiers in Ecology and Evolution. 2021 Jul 2;9:666564.]

* [http://jommid.pasteur.ac.ir/browse.php?a_id=345&sid=1&slc_lang=en&ftxt=0 Sefid F, Khalesi B, Mansoori B, Fotovvat M, Touhidinia M. Enhancement of SARS-CoV-2 Receptor Binding Domain-CR3022 Human Antibody Binding Affinity via In silico Engineering Approach. Journal of Medical Microbiology and Infectious Diseases. 2021 Sep 10;9(3):156-69.]

* [https://link.springer.com/article/10.1007/s10725-021-00735-3 Brunoni F, Rolli E, Polverini E, Spíchal L, Ricci A. The adjuvant activity of two urea derivatives on cytokinins: An example of serendipitous dual effect. Plant Growth Regulation. 2021 Nov;95:169-90.]

==2016-2020==

==={{Font color|#ff8000|Education & Communication}}===

<ref group="xtra">PMID: 32077575</ref><references group="xtra" />
<blockquote>
<span style="background-color:#fffce0;">Lee ''et al.'', 2020, said "... browser-based applications or interfaces (e.g., ''FirstGlance in Jmol'') increase accessibility for students. Hands-on use of visualization software by students seems to benefit their 3D understanding of proteins better than simply viewing it on-screen."</span>
</blockquote>

* [https://pubs.acs.org/doi/10.1021/acs.jchemed.8b00426 Cation−Π Interactions in Biochemistry: A Primer, Miguel O. Mitchell and John Means, J. Chem. Educ. 2018, 95, 12, 2284–2288.]

<ref group="xtra">PMID: 28214437</ref><references group="xtra" />

==={{Font color|#00b000|BioMedical Research}}===
====2020====
<table align="right"><tr><td>
[[Image:Lin et al 2020 Fig2d 1hk0.png|300px]]
</td><td width="250">
Fig. 2d from Lin ''et al.'', 2020. '''Secondary structure percentages''' and molecular rendering by ''FirstGlance in Jmol''.
Reproduced in accord with the Creative Commons Attribution-NonCommercial 4.0 International
Deed<ref name="ccanc4i">This work was published under the [https://creativecommons.org/licenses/by-nc/4.0/ Creative Commons Attribution-NonCommercial 4.0 International Deed].</ref>.
</td></tr></table>
<ref group="xtra">PMID: 33460241</ref><references group="xtra" />

<ref group="xtra">PMID: 31702846</ref><references group="xtra" />
<blockquote>
<span style="background-color:#fffce0;">Ben Chorin ''et al.'', 2020, wrote "The '''conservation grades (colors) are mapped onto the three-dimensional structure of the query protein''', which can be viewed using ... FirstGlance in Jmol. This visualization is highly enlightening because it emphasizes the important, evolutionarily conserved regions of the protein."</span>
</blockquote>

<ref group="xtra">PMID: 31608807</ref><references group="xtra" />

<table align="right"><tr><td>
[[Image:McGurk et la 2020 Fig 2I,J tankyrase-binding domain halos 4bs2.png|500px]]
</td><td width="250">
Portions of Fig. 2I,J from McGurk ''et al.'', 2020. The '''tankyrase-binding-domain of [[4bs2]] was identified ({{Yelspan|yellow halos}}) with the ''Find'' tool''' of ''FirstGlance in Jmol''. ''FirstGlance'' also added the sequence labels.
Reproduced in accord with the Creative Commons Attribution 4.0 International
Deed<ref name="cca4i" />.
</td></tr></table>
<ref group="xtra">PMID: 32409565</ref><references group="xtra" />

<ref group="xtra">PMID: 32531564</ref><references group="xtra" />

<ref group="xtra">PMID: 32706779</ref><references group="xtra" />
<blockquote>
<span style="background-color:#fffce0;">Shalit and Tuvi-Arad, 2020, wrote "For each protein [565 were analyzed], we calculated the Rfree grade as defined by FirstGlance in Jmol .... '''Files were kept if their Rfree grade was at least "average" at their resolution.'''"</span>
</blockquote>

<ref group="xtra">PMID: 32123543</ref><references group="xtra" />
<blockquote>
<span style="background-color:#fffce0;">Mattila ''et al.'' 2020 provided a downloadable PDB file with a link to view it by uploading to ''FirstGlance in Jmol''.</span>
</blockquote>

<ref group="xtra">PMID: 32867961</ref><references group="xtra" />

* [http://op.niscpr.res.in/index.php/IJBB/article/viewFile/29116/465477657 Zaheer ZA, Sankaranarayanan K. In silico analysis of κ-theraphotoxin-Cg2a from Chilobrachys guangxiensis. Indian Journal of Biochemistry and Biophysics (IJBB). 2020 Jul 28;57(4):458-66.]

====2019====
<ref group="xtra">PMID: 31058389</ref><references group="xtra" />

<ref group="xtra">PMID: 31172379</ref><references group="xtra" />

<ref group="xtra">PMID: 31018129</ref><references group="xtra" />

<ref group="xtra">PMID: 30791384</ref><references group="xtra" />

====2018====
<ref group="xtra">PMID: 30346734</ref><references group="xtra" />

<ref group="xtra">PMID: 29534001</ref><references group="xtra" />

<ref group="xtra">PMID: 29567208</ref><references group="xtra" />

<ref group="xtra">PMID: 30398106</ref><references group="xtra" />

<ref group="xtra">PMID: 29684709</ref><references group="xtra" />

<ref group="xtra">PMID: 29704154</ref><references group="xtra" />

<ref group="xtra">PMID: 30381731</ref><references group="xtra" />

* [https://link.springer.com/article/10.1134/S1068162018020024 Podlesnykh SV, Shanshin DV, Kolosova EA, Murashkin DE, Shaprova ON, Shcherbakov DN, Chapoval AI. Development of Search Strategy for Peptide Inhibitors of Immune Checkpoints. Russian Journal of Bioorganic Chemistry. 2018 Mar;44:150-7.]

====2017====

<ref group="xtra">PMID: 29262419</ref><references group="xtra" />

<ref group="xtra">PMID: 28791129</ref><references group="xtra" />

<ref group="xtra">PMID: 29079705</ref><references group="xtra" />

<ref group="xtra">PMID: 28302399</ref><references group="xtra" />

<ref group="xtra">PMID: 28872841</ref><references group="xtra" />

<ref group="xtra">PMID: 28434129</ref><references group="xtra" />

<ref group="xtra">PMID: 30258911</ref><references group="xtra" />

====2016====

* [https://www.researchgate.net/profile/Rahul-Shelake/publication/309241483_Structural_Analysis_and_Homology_Modeling_of_Members_of_smt-like_Operon_from_Thermophilic_Cyanobacterium_Thermosynechococcus_elongatus_BP-1/links/58099b9708ae1c98c25263e3/Structural-Analysis-and-Homology-Modeling-of-Members-of-smt-like-Operon-from-Thermophilic-Cyanobacterium-Thermosynechococcus-elongatus-BP-1.pdf Shelake RM, Hayashi H, Morita EH. Structural analysis and homology modeling of members of smt-like operon from thermophilic cyanobacterium Thermosynechococcus elongatus BP-1. J Proteins Proteomics. 2016;7(3):221-30.]

<ref group="xtra">PMID: 27400707</ref><references group="xtra" />

<ref group="xtra">PMID: 26866676</ref><references group="xtra" />
<blockquote>
<span style="background-color:#fffce0;">See Figure 2 which uses ''FirstGlance in Jmol'' to '''highlight critical lysine residues''' in nucleosome histones with yellow halos. That Figure is not reproduced here because ACS denies permission to non-profit organizations, unless payment is made.</span>
</blockquote>

<ref group="xtra">PMID: 26043781</ref><references group="xtra" />
<blockquote>
<span style="background-color:#fffce0;">''FirstGlance in Jmol'' was used to '''locate and count charged residues'''.</span>
</blockquote>

<ref group="xtra">PMID: 27347491</ref><references group="xtra" />

* [https://www.academia.edu/download/79451787/medicinalchemistry-2-1016.pdf Santiago-Ruiz S, Polverini E, Manjarrez J, Espinoza KA, Reynoso E, Rivero IA. Virtual Screening of Putative Anticonvulsant Hydantoin Derived Drugs and Biological Evaluation. Ann. Med. Chem. Res. 2016;2(1):1016-23.]

<ref group="xtra">PMID: 26608339</ref><references group="xtra" />

==2011-2015==

===Coverage===
<table style="background-color:#ffe0e0;"><tr><td>
Coverage is nearly complete for the most recent decade 2016-2025 (above), as far as publications found with the methods used<ref name="gsmethods">In scholar.google.com, the query ''firstglance'' finds mostly irrelevant papers with the term ''first glance''. Quoting the query, ''"firstglance"'' was used to restrict hits to that exact single word. However, some papers erroneously cite ''First Glance in Jmol'', or even say something like ''Jmol, with the First Glance''. Therefore, a second search was done using ''"first glance" and jmol''.</ref> in [https://scholar.google.com Google Scholar]. For years before 2016 (below), only an arbitrary subset of citations is listed.
</td></tr></table>

==={{Font color|#ff8000|Education & Communication}}===

<ref group="xtra">PMID: 24591499</ref><references group="xtra" />
<blockquote>
<span style="background-color:#fffce0;">Barber & Stark wrote "FirstGlance in Jmol is a simple platform with sophisticated functionality for viewing a molecule's structure with different diagrams, cross-sections, and emphasis on various molecular features."</span>
</blockquote>

<ref group="xtra">PMID: 24979189</ref><references group="xtra" />

<ref group="xtra">PMID: 23649886</ref><references group="xtra" />

* [https://onlinelibrary.wiley.com/doi/abs/10.1002/ijch.201300024 Hanson RM, Prilusky J, Renjian Z, Nakane T, Sussman JL. JSmol and the next‐generation web‐based representation of 3D molecular structure as applied to proteopedia. Israel Journal of Chemistry. 2013 Apr;53(3‐4):207-16.]

<ref group="xtra">PMID: 23354749</ref><references group="xtra" />
<blockquote>
<span style="background-color:#fffce0;">Forest writes "Structures should be made to come alive in articles. ... [A] straightforward option is to include a link to the NSF-supported Java-based application ''Firstglance in Jmol'' that will allow the reader to call up the pdb file in a simple Web-based viewer that is browser independent."</span>
</blockquote>

<ref group="xtra">PMID: 24019219</ref><references group="xtra" />
<blockquote>
<span style="background-color:#fffce0;">Figure 1 is an excellent example of how a student used ''FirstGlance in Jmol'' to '''visualize hydrophobic cores'''. That Figure is not reproduced here because obtaining permission from Wiley Publications is complicated and may require payment even for a non-profit educational organization with open access on the Internet.</span>
</blockquote>

<ref group="xtra">PMID: 23166023</ref><references group="xtra" />
<blockquote>
<span style="background-color:#fffce0;">''FirstGlance in Jmol'' was the sole 3D visualization tool provided to students in this study.</span>
</blockquote>

* [https://pubs.acs.org/doi/full/10.1021/ed101022g Saderholm, Matthew, and Anthony Reynolds. "Jmol-enhanced biochemistry research projects." Journal of Chemical Education 88.8 (2011): 1074-1078.].

==={{Font color|#00b000|BioMedical Research}}===
<span style="background-color:#ffe0e0;">[[#Coverage|Partial Coverage]]</span>

<ref group="xtra">PMID: 25785714</ref><references group="xtra" />

<ref group="xtra">PMID: 26224535</ref><references group="xtra" />

<table align="right"><tr><td>
[[Image:Chen et al 2012 Fig 1 3g04.png|500px]]
</td><td width="250">
Fig. 1 from Chen ''et al.'', 2012. Atomic rendering of the leucine-rich repeat domain of the thyroid-stimulating hormone receptor by ''FirstGlance in Jmol'' showing hydrophobic vs. polar regions and charge distribution.
Yellow halos highlight charged residues at the C-terminal "base" of the domain.
Reproduced in accord with the Creative Commons Attribution 4.0 International
Deed<ref name="cca4i" />.
</td></tr></table>

<ref group="xtra">PMID: 25336027</ref><references group="xtra" />

<ref group="xtra">PMID: 24692644</ref><references group="xtra" />

* [https://pubs.acs.org/doi/abs/10.1021/bk-2013-1142.ch016 Fleming SA. Teaching tools for organic and bio-organic chemistry. In Pedagogic Roles of Animations and Simulations in Chemistry Courses 2013 (pp. 389-409). American Chemical Society.]

<ref group="xtra">PMID: 22359649</ref><references group="xtra" />

<ref group="xtra">PMID: 22235356</ref><references group="xtra" />

<ref group="xtra">PMID: 23119066</ref><references group="xtra" />

<ref group="xtra">PMID: 22069494</ref><references group="xtra" />

<ref group="xtra">PMID: 21472436</ref><references group="xtra" />
<blockquote>
<span style="background-color:#fffce0;">In 2011, the '''Protein Structure Initiative's''' Structural Biology '''Knowledgebase''' offers ''FirstGlance in Jmol'' as a structure viewer.</span>
</blockquote>

<ref group="xtra">PMID: 22440564</ref><references group="xtra" />

==2006-2010==

==={{Font color|#ff8000|Education & Communication}}===
<span style="background-color:#ffe0e0;">[[#Coverage|Partial Coverage]]</span>

<ref group="xtra">PMID: 21567875</ref><references group="xtra" />
<blockquote>
<span style="background-color:#fffce0;">... applications such as the excellent, FirstGlance in Jmol provide a quick and simple way to view and manipulate structures ....</span>
</blockquote>

<ref group="xtra">PMID: 20504857</ref><references group="xtra" />
<blockquote>
<span style="background-color:#fffce0;">Porollo and Meller wrote "Protein–ligand contacts are determined using the respective procedure adopted in Protein Explorer and subsequently in the FirstGlance in Jmol server (FGiJ) that accounts for hydrogen bonds, water and salt bridges, hydrophobic and aromatic ring interaction and different types of metals binding. For the corresponding bond distance definitions, the reader is referred to the FGiJ documentation." '''This excellent server continues to be available in 2025''' as [https://polyview.cchmc.org/polyview3d.html PolyView-3D], and is linked at the Martz website [http://molviz.org MolviZ.Org].</span>
</blockquote>

<ref group="xtra">PMID: 20541422</ref><references group="xtra" />

<ref group="xtra">PMID: 20195256</ref><references group="xtra" />

<ref group="xtra">PMID: 21567685</ref><references group="xtra" />
<blockquote>
<span style="background-color:#fffce0;">''FirstGlance in Jmol'' was the primary visualization package provided to students in this curriculum.</span>
</blockquote>

<ref group="xtra">PMID: 19230677</ref><references group="xtra" />
<blockquote>
<span style="background-color:#fffce0;">Hodis and Sussman wrote "... widely available
molecular visualization programs ... are
often inaccessible to non-specialists owing to a steep learning curve (with, in our opinion, FirstGlance in Jmol being an exception)."</span>
</blockquote>

<ref group="xtra">PMID: 19847312</ref><references group="xtra" />

* [https://pmc.ncbi.nlm.nih.gov/articles/PMC2762578/ Palmer III AG, Matthews BW. Interactive graphics return to protein science. Protein Science: A Publication of the Protein Society. 2009 Mar 20;18(4):677.]

<ref group="xtra">PMID: 19461848</ref><references group="xtra" />
<blockquote>
<span style="background-color:#fffce0;">Interactivity allows a reader unbounded scope to explore a structure, taking advantage of whatever features the visualization software may provide. This is the basis underlying FirstGlance in Jmol, a service that an increasing number of journals link to, which provides standard buttons to view different aspects of a protein structure ....</span>
</blockquote>

<ref group="xtra">PMID: 21638687</ref><references group="xtra" />
<blockquote>
<span style="background-color:#fffce0;">Herráez said "I express my gratitude to Prof. Eric Martz (University of Massachusetts), long-time advocate of molecular modeling teaching, provider of Rasmol and Chime information and support on his website, of teaching-oriented recommendations and sample materials, of the excellent Protein Explorer software for macromolecule visualization and analysis, and of other countless contributions, including the recent FirstGlance in Jmol."</span>
</blockquote>

==={{Font color|#00b000|BioMedical Research}}===
<span style="background-color:#ffe0e0;">[[#Coverage|Partial Coverage]]</span>

<ref group="xtra">PMID: 20634950</ref><references group="xtra" />
<blockquote>
<span style="background-color:#fffce0;">''FirstGlance in Jmol'' was used to visualize patterns of '''evolutionary conservation''' calculated by the [http://consurf.tau.ac.il ConSurf Server].</span>
</blockquote>

<ref group="xtra">PMID: 21029378</ref><references group="xtra" />

<ref group="xtra">PMID: 18971256</ref><references group="xtra" />

<ref group="xtra">PMID: 19329630</ref><references group="xtra" />

<ref group="xtra">PMID: 19233205</ref><references group="xtra" />

* [https://books.google.com/books?hl=en&lr=&id=3jq1kSKcvEAC&oi=fnd&pg=PR11&dq=firstglance&ots=XchA-jpK7C&sig=TKhk00SK4YHR3QtLqXZU23d0jK8 Courey AJ. Mechanisms in transcriptional regulation. John Wiley & Sons; 2009 Jan 22.]
<blockquote>
<span style="background-color:#fffce0;">"''FirstGlance in Jmol'': This free program, also developed by Eric Martz, is probably '''the easiest way to look at macromolecules'''."</span>
</blockquote>

<ref group="xtra">PMID: 18067320</ref><references group="xtra" />
<blockquote>
<span style="background-color:#fffce0;">"The "'''contact residues'''" of the SH3 domain with the ligand were assigned by means of the FirstGlance in Jmol program ...."</span>
</blockquote>

<ref group="xtra">PMID: 19081051</ref><references group="xtra" />

<ref group="xtra">PMID: 18347046</ref><references group="xtra" />

==Journals Cited==

Peer-reviewed scientific papers listed above that cite ''FirstGlance in Jmol'' were published in numerous journals, including
===Education Journals===
''Biochemistry and Molecular Biology Education (8), Journal of Chemical Education.''

===Basic Research Journals===
''ACS Chemical Biology, Archives of Biophysics & Biochemistry, Biochemistry (3), BMC Microbiology, Cell Reports, Current Opinion in Virology, European Journal of Cell Biology, FEBS Journal, Gene, Journal of Cell Science, Journal of Bacteriology (2), Journal of Biological Chemistry, Journal of Molecular Biology, Molecular Microbiology, Nature Methods, Nucleic Acids Research (2), Planta, Plant Growth Regulation, Plant Cell Reports, PLOS One (9), Protein Science (3), Structure*, Scientific Reports, Trends in Biochemical Sciences (2), Veterinary Journal''.

<nowiki>*</nowiki> Nimrod ''et al.'', 2008.

===Medical Journals===
''Annals of Neurology, Infection & Immunity, Leukemia, Medical Microbiology & Immunology, PLOS Neglected Tropical Diseases.''

==References==
<references />

FirstGlance in Jmol Literature Citations

2026-07-17T19:46:38Z

Eric Martz:

The following publications in the scientific literature cite use of ''[[FirstGlance in Jmol]]''. This list excludes publications co-authored by [[User:Eric Martz]], the author of ''FirstGlance in Jmol''. (Those are listed at [https://scholar.google.com/citations?user=Bb3H0OsAAAAJ&hl=en&oi=ao Google Scholar: Eric Martz].) The 120 citations listed below in more than 30 [[#Journals Cited|peer-reviewed journals]] were found by searching full text using [https://scholar.google.com Google Scholar] (see [[#Coverage|Coverage]]), and all were verified to cite ''FirstGlance in Jmol''.
<table align="right" class="wikitable" width="500"><tr><td>
[[FirstGlance in Jmol]] offers, since 2006, free visualization and analysis of protein molecules and other macromolecules (DNA, RNA, oligosaccharides, etc.). It is easy to use and provides built-in guidance and help. In 2024, it was used on average '''265 times/day'''. For more, see
* [[FirstGlance in Jmol]]
* [http://firstglance.jmol.org/whatis.htm#unique Unique Capabilities of FirstGlance in Jmol]
* [https://www.youtube.com/@ericmartz9100 FirstGlance YouTube Channel] [[Image:Youtube.png]]
* [[FirstGlance/Index]], a list of resources about FirstGlance in Jmol, including all the relevant pages in Proteopedia.
* [http://firstglance.jmol.org Start FirstGlance in Jmol]
</td></tr></table>
Researchers took advantage of [http://firstglance.jmol.org/whatis.htm#unique unique capabilities] of ''FirstGlance'':
<ul>
<li>Visual analysis of structures predicted by '''AlphaFold2''', colored by '''reliability''' estimates.
<li>Calculation of average '''pLDDT''' for structures predicted by '''AlphaFold3'''.
<li>Seeing locations of [[Missing residues and incomplete sidechains|'''missing''' residues]], which affect shape, distribution of polar/hydrophobic surfaces, and may result in missing [[salt bridges]] and [[cation-pi interactions]].
<li>Locating '''mutations''' in the 3D model.
<li>Positions of proteins in lipid bilayer '''membranes''' (models from [https://opm.phar.umich.edu/ OPM U. Mich.]).
<li>Coloring amino acids by evolutionary '''conservation''' (determined by [https://consurf.tau.ac.il ConSurf]) to identify functional sites.
<li>Rejection of models with '''Rfree''' below average for their resolutions.
<li>Applying sequence '''numbering''' to the 3D view.
<li>Seeing the distribution of hydrophobic vs. '''polar''' amino acids.
<li>Percentages of '''secondary''' structure elements.
<li>Locating residues or regions of interest, using ''Find'' to apply yellow '''halos'''.
<li>Distribution and counts of '''charged''' residues.
<li>Visual '''isolation''' of domains or regions of interest.
<li>Identification of '''contact residues'''.
</ul>
<span style="background-color:#fffce0;">Use your browser's ''Find in page'' (Control-f / Command-f) to locate studies involving the '''bold''' terms above. Some of these capabilities are illustrated with animations generated by ''FirstGlance'' at [https://tinyurl.com/movingmolecules tinyurl.com/movingmolecules].</span>
__NOTOC__

==2026==

==={{Font color|#ff8000|Education & Communication}}===

<ref group="xtra">PMID: 41854287</ref><references group="xtra" />

==={{Font color|#00b000|BioMedical Research}}===

<ref group="xtra">PMID: 42344113</ref><references group="xtra" />

<ref group="xtra">PMID: 41504448</ref><references group="xtra" />

==2021-2025==

==={{Font color|#ff8000|Education & Communication}}===

<ref group="xtra">PMID: 39976303</ref><references group="xtra" />

* [https://www.google.com/books/edition/Food_Chemistry_in_Small_Bites/QLk_EQAAQBAJ O'Hara, Patricia B. Food Chemistry in Small Bites: The Alchemist in the Kitchen. Univ of California Press; 2025 Apr 15.]

<ref group="xtra">PMID: 39291955</ref><references group="xtra" />

<ref group="xtra">PMID: 35001912</ref><references group="xtra" />

==={{Font color|#00b000|BioMedical Research}}===
====2025====
<ref group="xtra">PMID: 41390121</ref><references group="xtra" />

<ref group="xtra">PMID: 41060696</ref><references group="xtra" />
<blockquote><span style="background-color:#fffce0;">
For AlphaFold3-predicted structures, "Average '''pLDDT''' scores were calculated using FirstGlance in Jmol."
</span>
</blockquote>

<ref group="xtra">PMID: 41331102</ref><references group="xtra" />

<ref group="xtra">PMID: 41047069</ref><references group="xtra" />

<ref group="xtra">PMID: 41072766</ref><references group="xtra" />

<table align="right"><tr><td>
[[Image:Sefid-consurf-teplizumab-2025.png]]
</td><td width="250">
Figure 2 from Sefid ''et al.'', 2025.
'''Conservation''' of amino acids in Teplizumab analyzed using the ConSurf Server and displayed by FirstGlance in Jmol.
Reproduced in accord with the Creative Commons Attribution Deed<ref name="cca4i" />
</td></tr></table>
* [https://d1wqtxts1xzle7.cloudfront.net/123175184/4_DR_sefid-libre.pdf Sefid F, Monshizadeh K, Ghenaatzadeh R, Roodgarpour Z, Azamirad G, Mirhosseini H. Antibody Engineering Toward Enhancement of Teplizumab Anti-CD3 Binding Affinity in Type 1 Diabetes Prevention and Treatment. Iranian Journal of Diabetes and Obesity. 2025 May 10;17(2):97-109.]

<table align="right"><tr><td>
[[Image:Garcia-e-lyta-fig5-microorgs2025.png|300px]]
</td><td width="250">
Figure 5 from García, 2025. Molecular rendering of [[4x36]] by FirstGlance in Jmol. Reproduced with written permission from Ernesto Garcia (April 29, 2025).
</td></tr></table>
<ref group="xtra">PMID: 40284663</ref><references group="xtra" />

<ref group="xtra">PMID: 39299531</ref><references group="xtra" />

* [https://www.biorxiv.org/content/10.1101/2025.04.11.648320v1.full Weber H, Ehinger A, Kolb D, Fallahzadeh-Mamaghani V, Halter T, Franz-Wachtel M, zur Oven-Krockhaus S, Gronnier J, Zipfel C, Harter K, Kemmerling B. Arabidopsis HYPERSENSITIVE INDUCED REACTION 2 affects plasma membrane receptor pathways and organization. bioRxiv. 2025:2025-04.]
<blockquote>
<span style="background-color:#fffce0;">"AlphaFold2 modeling of HIR2 and analysis of the '''distribution of polar amino acids by FirstGlance''' revealed an N-terminal surface-exposed platform of HIR2 that consists of nonpolar residues, which could interact with hydrophobic parts of the (plasma) membrane."</span>
</blockquote>

<ref group="xtra">PMID: 39758030</ref><references group="xtra" />

====2024====
<table align="right"><tr><td>
[[Image:Martinez-alcantar-2024-fig1-1ol5.png|500px]]
</td><td width="250">
Fig. 1, [[1ol5]], from Martinez ''et al.'', 2024. Molecular rendering and Å scale by FirstGlance in Jmol; black labels added by Martinez ''et al.''.
Reproduced in accord with the Creative Commons Attribution Deed<ref name="cca4i">This work was published under the [https://creativecommons.org/licenses/by/4.0/ Creative Commons Attribution 4.0 International Deed].</ref>.
</td></tr></table>

<ref group="xtra">PMID: 39636801</ref><references group="xtra" />
<blockquote>
<span style="background-color:#fffce0;">FirstGlance in Jmol was used to visualize and tabulate '''missing residues''' in [[2az5]].</span>
(See [[Missing residues and incomplete sidechains]].)
</blockquote>

* [https://publish.kne-publishing.com/index.php/IJDO/article/view/15710 Sefid, Fateme, et al. "Antibody Engineering to Enhancement of Ranibizumab Binding Affinity for the Prevention and Treatment of Diabetic Retinopathy." Iranian journal of diabetes and obesity (2024).]

<ref group="xtra">PMID: 37904054</ref><references group="xtra" />

* [https://www.mdpi.com/2813-3757/2/4/23 Martínez-Alcantar, Lorena, et al. "Cyclic Peptides as Protein Kinase Modulators and Their Involvement in the Treatment of Diverse Human Diseases." Kinases and Phosphatases 2.4 (2024): 346-378.]

<ref group="xtra">PMID: 38968704</ref><references group="xtra" />
<blockquote>
<span style="background-color:#fffce0;">FirstGlance was used to visualize models predicted by '''AlphaFold2, colored by reliablity scores'''.</span>
</blockquote>

<table align="right"><tr><td>
[[Image:Gajta et al 2024 Fig3C Isolated domain from AlphaFold2.png|400px]]
</td><td width="250">
Fig. 3C, and AlphaFold2 prediction, from Gajda ''et al.'', 2024. Isolation of this domain, sequence numbering (applied with a single checkbox), and molecular rendering by FirstGlance in Jmol.
Reproduced in accord with the Creative Commons Attribution Deed<ref name="cca4i" />.
</td></tr></table>

<ref group="xtra">PMID: 38731903</ref><references group="xtra" />

<ref group="xtra">PMID: 39052973</ref><references group="xtra" />
<blockquote>
<span style="background-color:#fffce0;">'''Transmembrane secondary structure segments''' were evaluated using FirstGlance prior to docking analysis.</span>
</blockquote>

* [https://onlinelibrary.wiley.com/doi/full/10.1155/2024/1575103 Pan Y, Yao X, Yang TN, Li JL, Shi DF. The VP1/2 Protein of a New Recombinant PRV Strain Promotes the Infectivity and Pathogenicity of PRV in Northeastern China. Transboundary and Emerging Diseases. 2024;2024(1):1575103.]
<blockquote>
<span style="background-color:#fffce0;">FirstGlance was used to '''locate mutations''' in the 3D structure.</span>
</blockquote>

====2023====

<ref group="xtra">PMID: 37154976</ref><references group="xtra" />

<ref group="xtra">PMID: 37464933</ref><references group="xtra" />

* [https://www.biorxiv.org/content/10.1101/2023.05.28.542320.abstract Sondhi Y, Messcher RL, Bellantuano AJ, Storer CG, Cinel SD, Godfrey RK, Glass D, St Laurent RA, Hamilton CA, Earl C, Brislawn CJ. The developmental gene disco regulates diel-niche evolution in adult moths. bioRxiv. 2023 May 28:2023-05.]

* [https://dc.etsu.edu/context/etd/article/5760/viewcontent/PremaA052323f.pdf Prema A. Mapping The Binding Site Within Integrin αD β2 for Carboxyethylpyrrole (CEP)-Modified Proteins (2023). Electronic Theses and Dissertations, East Tennessee State University. Paper 4232.]

* [https://link.springer.com/article/10.1007/s11816-022-00788-4 Hassan MM, Martin S, Feng K, Yates TB, Yuan G, Martin MZ, Martin S, Muchero W, Griffiths NA, Weston DJ, Yang X. Genome-wide identification and functional prediction of silicon (Si) transporters in poplar (Populus trichocarpa). Plant Biotechnology Reports. 2023 Apr;17(2):285-302.]

<ref group="xtra">PMID: 36670408</ref><references group="xtra" />

====2022====
<table align="right"><tr><td>
[[Image:Puccio-2021-mol-micro.png|300px]]
</td><td width="250">
Graphical Abstract from Puccio ''et al.'', 2022. Molecular rendering by FirstGlance in Jmol. <font color="red">'''Red'''</font> and <font color="blue">'''Blue'''</font> planes represent boundaries of the lipid bilayer membrane. Reproduced in accord with the Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International
Deed<ref name="ccannd4i">This work was published under the [https://creativecommons.org/licenses/by-nc-nd/4.0/ Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International Deed].</ref>.
</td></tr></table>
<ref group="xtra">PMID: 34855265</ref><references group="xtra" />
<blockquote>
<span style="background-color:#fffce0;">"'''Positions within a cellular membrane''' were predicted using OPM (https://opm.phar.umich.edu/) and visualized in JMol 3.0 using FirstGlance."</span>
</blockquote>

<ref group="xtra">PMID: 35869579</ref><references group="xtra" />

<ref group="xtra">PMID: 36120551</ref><references group="xtra" />

<ref group="xtra">PMID: 35537348</ref><references group="xtra" />

<table align="right"><tr><td>
[[Image:Camelo, lopez-pazos 2022 fig 7-CClic.png|400px]]
</td><td width="250">
Figure 5 from Camelo ''et al.'', 2025. Molecular rendering by FirstGlance in Jmol. Reproduced in accord with the Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International
Deed<ref name="ccansa4i">This work was published under the [https://creativecommons.org/licenses/by-nc-sa/4.0/deed.en Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International Deed].</ref>.
</td></tr></table>
* [http://scielo.senescyt.gob.ec/scielo.php?pid=S1390-85962022000200032&script=sci_abstract&tlng=en Lozano Camelo OC, Rojas Arias AC, Ávila Méndez KJ, López-Pazos SA. Preservación modificada y descripción de la fungalisina para Batrachochytrium dendrobatidis. LA GRANJA. Revista de Ciencias de la Vida. 2022 Feb;36(2):32-44.]

<ref group="xtra">PMID: 35493110</ref><references group="xtra" />

<ref group="xtra">PMID: 35742992</ref><references group="xtra" />

* [https://dl.acm.org/doi/abs/10.1145/3570773.3570833 Xu Y. The Analysis of Tiotropium bromide and Roflumilast: Two Potent Medications for Chronic Obstructive Pulmonary Disease. InProceedings of the 3rd International Symposium on Artificial Intelligence for Medicine Sciences 2022 Oct 13 (pp. 231-238).]

<ref group="xtra">PMID: 35228627</ref><references group="xtra" />

<ref group="xtra">PMID: 35139120</ref><references group="xtra" />

====2021====

<ref group="xtra">PMID: 34619810</ref><references group="xtra" />

<ref group="xtra">PMID: 32496928</ref><references group="xtra" />

<ref group="xtra">PMID: 34786595</ref><references group="xtra" />

* [https://www.frontiersin.org/articles/10.3389/fevo.2021.666564/full Junker N, Gossmann TI. Adaptation-driven evolution of sirtuin 1 (SIRT1), a key regulator of metabolism and aging, in marmot species. Frontiers in Ecology and Evolution. 2021 Jul 2;9:666564.]

* [http://jommid.pasteur.ac.ir/browse.php?a_id=345&sid=1&slc_lang=en&ftxt=0 Sefid F, Khalesi B, Mansoori B, Fotovvat M, Touhidinia M. Enhancement of SARS-CoV-2 Receptor Binding Domain-CR3022 Human Antibody Binding Affinity via In silico Engineering Approach. Journal of Medical Microbiology and Infectious Diseases. 2021 Sep 10;9(3):156-69.]

* [https://link.springer.com/article/10.1007/s10725-021-00735-3 Brunoni F, Rolli E, Polverini E, Spíchal L, Ricci A. The adjuvant activity of two urea derivatives on cytokinins: An example of serendipitous dual effect. Plant Growth Regulation. 2021 Nov;95:169-90.]

==2016-2020==

==={{Font color|#ff8000|Education & Communication}}===

<ref group="xtra">PMID: 32077575</ref><references group="xtra" />
<blockquote>
<span style="background-color:#fffce0;">Lee ''et al.'', 2020, said "... browser-based applications or interfaces (e.g., ''FirstGlance in Jmol'') increase accessibility for students. Hands-on use of visualization software by students seems to benefit their 3D understanding of proteins better than simply viewing it on-screen."</span>
</blockquote>

* [https://pubs.acs.org/doi/10.1021/acs.jchemed.8b00426 Cation−Π Interactions in Biochemistry: A Primer, Miguel O. Mitchell and John Means, J. Chem. Educ. 2018, 95, 12, 2284–2288.]

<ref group="xtra">PMID: 28214437</ref><references group="xtra" />

==={{Font color|#00b000|BioMedical Research}}===
====2020====
<table align="right"><tr><td>
[[Image:Lin et al 2020 Fig2d 1hk0.png|300px]]
</td><td width="250">
Fig. 2d from Lin ''et al.'', 2020. '''Secondary structure percentages''' and molecular rendering by ''FirstGlance in Jmol''.
Reproduced in accord with the Creative Commons Attribution-NonCommercial 4.0 International
Deed<ref name="ccanc4i">This work was published under the [https://creativecommons.org/licenses/by-nc/4.0/ Creative Commons Attribution-NonCommercial 4.0 International Deed].</ref>.
</td></tr></table>
<ref group="xtra">PMID: 33460241</ref><references group="xtra" />

<ref group="xtra">PMID: 31702846</ref><references group="xtra" />
<blockquote>
<span style="background-color:#fffce0;">Ben Chorin ''et al.'', 2020, wrote "The '''conservation grades (colors) are mapped onto the three-dimensional structure of the query protein''', which can be viewed using ... FirstGlance in Jmol. This visualization is highly enlightening because it emphasizes the important, evolutionarily conserved regions of the protein."</span>
</blockquote>

<ref group="xtra">PMID: 31608807</ref><references group="xtra" />

<table align="right"><tr><td>
[[Image:McGurk et la 2020 Fig 2I,J tankyrase-binding domain halos 4bs2.png|500px]]
</td><td width="250">
Portions of Fig. 2I,J from McGurk ''et al.'', 2020. The '''tankyrase-binding-domain of [[4bs2]] was identified ({{Yelspan|yellow halos}}) with the ''Find'' tool''' of ''FirstGlance in Jmol''. ''FirstGlance'' also added the sequence labels.
Reproduced in accord with the Creative Commons Attribution 4.0 International
Deed<ref name="cca4i" />.
</td></tr></table>
<ref group="xtra">PMID: 32409565</ref><references group="xtra" />

<ref group="xtra">PMID: 32531564</ref><references group="xtra" />

<ref group="xtra">PMID: 32706779</ref><references group="xtra" />
<blockquote>
<span style="background-color:#fffce0;">Shalit and Tuvi-Arad, 2020, wrote "For each protein [565 were analyzed], we calculated the Rfree grade as defined by FirstGlance in Jmol .... '''Files were kept if their Rfree grade was at least "average" at their resolution.'''"</span>
</blockquote>

<ref group="xtra">PMID: 32123543</ref><references group="xtra" />
<blockquote>
<span style="background-color:#fffce0;">Mattila ''et al.'' 2020 provided a downloadable PDB file with a link to view it by uploading to ''FirstGlance in Jmol''.</span>
</blockquote>

<ref group="xtra">PMID: 32867961</ref><references group="xtra" />

* [http://op.niscpr.res.in/index.php/IJBB/article/viewFile/29116/465477657 Zaheer ZA, Sankaranarayanan K. In silico analysis of κ-theraphotoxin-Cg2a from Chilobrachys guangxiensis. Indian Journal of Biochemistry and Biophysics (IJBB). 2020 Jul 28;57(4):458-66.]

====2019====
<ref group="xtra">PMID: 31058389</ref><references group="xtra" />

<ref group="xtra">PMID: 31172379</ref><references group="xtra" />

<ref group="xtra">PMID: 31018129</ref><references group="xtra" />

<ref group="xtra">PMID: 30791384</ref><references group="xtra" />

====2018====
<ref group="xtra">PMID: 30346734</ref><references group="xtra" />

<ref group="xtra">PMID: 29534001</ref><references group="xtra" />

<ref group="xtra">PMID: 29567208</ref><references group="xtra" />

<ref group="xtra">PMID: 30398106</ref><references group="xtra" />

<ref group="xtra">PMID: 29684709</ref><references group="xtra" />

<ref group="xtra">PMID: 29704154</ref><references group="xtra" />

<ref group="xtra">PMID: 30381731</ref><references group="xtra" />

* [https://link.springer.com/article/10.1134/S1068162018020024 Podlesnykh SV, Shanshin DV, Kolosova EA, Murashkin DE, Shaprova ON, Shcherbakov DN, Chapoval AI. Development of Search Strategy for Peptide Inhibitors of Immune Checkpoints. Russian Journal of Bioorganic Chemistry. 2018 Mar;44:150-7.]

====2017====

<ref group="xtra">PMID: 29262419</ref><references group="xtra" />

<ref group="xtra">PMID: 28791129</ref><references group="xtra" />

<ref group="xtra">PMID: 29079705</ref><references group="xtra" />

<ref group="xtra">PMID: 28302399</ref><references group="xtra" />

<ref group="xtra">PMID: 28872841</ref><references group="xtra" />

<ref group="xtra">PMID: 28434129</ref><references group="xtra" />

<ref group="xtra">PMID: 30258911</ref><references group="xtra" />

====2016====

* [https://www.researchgate.net/profile/Rahul-Shelake/publication/309241483_Structural_Analysis_and_Homology_Modeling_of_Members_of_smt-like_Operon_from_Thermophilic_Cyanobacterium_Thermosynechococcus_elongatus_BP-1/links/58099b9708ae1c98c25263e3/Structural-Analysis-and-Homology-Modeling-of-Members-of-smt-like-Operon-from-Thermophilic-Cyanobacterium-Thermosynechococcus-elongatus-BP-1.pdf Shelake RM, Hayashi H, Morita EH. Structural analysis and homology modeling of members of smt-like operon from thermophilic cyanobacterium Thermosynechococcus elongatus BP-1. J Proteins Proteomics. 2016;7(3):221-30.]

<ref group="xtra">PMID: 27400707</ref><references group="xtra" />

<ref group="xtra">PMID: 26866676</ref><references group="xtra" />
<blockquote>
<span style="background-color:#fffce0;">See Figure 2 which uses ''FirstGlance in Jmol'' to '''highlight critical lysine residues''' in nucleosome histones with yellow halos. That Figure is not reproduced here because ACS denies permission to non-profit organizations, unless payment is made.</span>
</blockquote>

<ref group="xtra">PMID: 26043781</ref><references group="xtra" />
<blockquote>
<span style="background-color:#fffce0;">''FirstGlance in Jmol'' was used to '''locate and count charged residues'''.</span>
</blockquote>

<ref group="xtra">PMID: 27347491</ref><references group="xtra" />

* [https://www.academia.edu/download/79451787/medicinalchemistry-2-1016.pdf Santiago-Ruiz S, Polverini E, Manjarrez J, Espinoza KA, Reynoso E, Rivero IA. Virtual Screening of Putative Anticonvulsant Hydantoin Derived Drugs and Biological Evaluation. Ann. Med. Chem. Res. 2016;2(1):1016-23.]

<ref group="xtra">PMID: 26608339</ref><references group="xtra" />

==2011-2015==

===Coverage===
<table style="background-color:#ffe0e0;"><tr><td>
Coverage is nearly complete for the most recent decade 2016-2025 (above), as far as publications found with the methods used<ref name="gsmethods">In scholar.google.com, the query ''firstglance'' finds mostly irrelevant papers with the term ''first glance''. Quoting the query, ''"firstglance"'' was used to restrict hits to that exact single word. However, some papers erroneously cite ''First Glance in Jmol'', or even say something like ''Jmol, with the First Glance''. Therefore, a second search was done using ''"first glance" and jmol''.</ref> in [https://scholar.google.com Google Scholar]. For years before 2016 (below), only an arbitrary subset of citations is listed.
</td></tr></table>

==={{Font color|#ff8000|Education & Communication}}===

<ref group="xtra">PMID: 24591499</ref><references group="xtra" />
<blockquote>
<span style="background-color:#fffce0;">Barber & Stark wrote "FirstGlance in Jmol is a simple platform with sophisticated functionality for viewing a molecule's structure with different diagrams, cross-sections, and emphasis on various molecular features."</span>
</blockquote>

<ref group="xtra">PMID: 24979189</ref><references group="xtra" />

<ref group="xtra">PMID: 23649886</ref><references group="xtra" />

* [https://onlinelibrary.wiley.com/doi/abs/10.1002/ijch.201300024 Hanson RM, Prilusky J, Renjian Z, Nakane T, Sussman JL. JSmol and the next‐generation web‐based representation of 3D molecular structure as applied to proteopedia. Israel Journal of Chemistry. 2013 Apr;53(3‐4):207-16.]

<ref group="xtra">PMID: 23354749</ref><references group="xtra" />
<blockquote>
<span style="background-color:#fffce0;">Forest writes "Structures should be made to come alive in articles. ... [A] straightforward option is to include a link to the NSF-supported Java-based application ''Firstglance in Jmol'' that will allow the reader to call up the pdb file in a simple Web-based viewer that is browser independent."</span>
</blockquote>

<ref group="xtra">PMID: 24019219</ref><references group="xtra" />
<blockquote>
<span style="background-color:#fffce0;">Figure 1 is an excellent example of how a student used ''FirstGlance in Jmol'' to '''visualize hydrophobic cores'''. That Figure is not reproduced here because obtaining permission from Wiley Publications is complicated and may require payment even for a non-profit educational organization with open access on the Internet.</span>
</blockquote>

<ref group="xtra">PMID: 23166023</ref><references group="xtra" />
<blockquote>
<span style="background-color:#fffce0;">''FirstGlance in Jmol'' was the sole 3D visualization tool provided to students in this study.</span>
</blockquote>

* [https://pubs.acs.org/doi/full/10.1021/ed101022g Saderholm, Matthew, and Anthony Reynolds. "Jmol-enhanced biochemistry research projects." Journal of Chemical Education 88.8 (2011): 1074-1078.].

==={{Font color|#00b000|BioMedical Research}}===
<span style="background-color:#ffe0e0;">[[#Coverage|Partial Coverage]]</span>

<ref group="xtra">PMID: 25785714</ref><references group="xtra" />

<ref group="xtra">PMID: 26224535</ref><references group="xtra" />

<table align="right"><tr><td>
[[Image:Chen et al 2012 Fig 1 3g04.png|500px]]
</td><td width="250">
Fig. 1 from Chen ''et al.'', 2012. Atomic rendering of the leucine-rich repeat domain of the thyroid-stimulating hormone receptor by ''FirstGlance in Jmol'' showing hydrophobic vs. polar regions and charge distribution.
Yellow halos highlight charged residues at the C-terminal "base" of the domain.
Reproduced in accord with the Creative Commons Attribution 4.0 International
Deed<ref name="cca4i" />.
</td></tr></table>

<ref group="xtra">PMID: 25336027</ref><references group="xtra" />

<ref group="xtra">PMID: 24692644</ref><references group="xtra" />

* [https://pubs.acs.org/doi/abs/10.1021/bk-2013-1142.ch016 Fleming SA. Teaching tools for organic and bio-organic chemistry. In Pedagogic Roles of Animations and Simulations in Chemistry Courses 2013 (pp. 389-409). American Chemical Society.]

<ref group="xtra">PMID: 22359649</ref><references group="xtra" />

<ref group="xtra">PMID: 22235356</ref><references group="xtra" />

<ref group="xtra">PMID: 23119066</ref><references group="xtra" />

<ref group="xtra">PMID: 22069494</ref><references group="xtra" />

<ref group="xtra">PMID: 21472436</ref><references group="xtra" />
<blockquote>
<span style="background-color:#fffce0;">In 2011, the '''Protein Structure Initiative's''' Structural Biology '''Knowledgebase''' offers ''FirstGlance in Jmol'' as a structure viewer.</span>
</blockquote>

<ref group="xtra">PMID: 22440564</ref><references group="xtra" />

==2006-2010==

==={{Font color|#ff8000|Education & Communication}}===
<span style="background-color:#ffe0e0;">[[#Coverage|Partial Coverage]]</span>

<ref group="xtra">PMID: 21567875</ref><references group="xtra" />
<blockquote>
<span style="background-color:#fffce0;">... applications such as the excellent, FirstGlance in Jmol provide a quick and simple way to view and manipulate structures ....</span>
</blockquote>

<ref group="xtra">PMID: 20504857</ref><references group="xtra" />
<blockquote>
<span style="background-color:#fffce0;">Porollo and Meller wrote "Protein–ligand contacts are determined using the respective procedure adopted in Protein Explorer and subsequently in the FirstGlance in Jmol server (FGiJ) that accounts for hydrogen bonds, water and salt bridges, hydrophobic and aromatic ring interaction and different types of metals binding. For the corresponding bond distance definitions, the reader is referred to the FGiJ documentation." '''This excellent server continues to be available in 2025''' as [https://polyview.cchmc.org/polyview3d.html PolyView-3D], and is linked at the Martz website [http://molviz.org MolviZ.Org].</span>
</blockquote>

<ref group="xtra">PMID: 20541422</ref><references group="xtra" />

<ref group="xtra">PMID: 20195256</ref><references group="xtra" />

<ref group="xtra">PMID: 21567685</ref><references group="xtra" />
<blockquote>
<span style="background-color:#fffce0;">''FirstGlance in Jmol'' was the primary visualization package provided to students in this curriculum.</span>
</blockquote>

<ref group="xtra">PMID: 19230677</ref><references group="xtra" />
<blockquote>
<span style="background-color:#fffce0;">Hodis and Sussman wrote "... widely available
molecular visualization programs ... are
often inaccessible to non-specialists owing to a steep learning curve (with, in our opinion, FirstGlance in Jmol being an exception)."</span>
</blockquote>

<ref group="xtra">PMID: 19847312</ref><references group="xtra" />

* [https://pmc.ncbi.nlm.nih.gov/articles/PMC2762578/ Palmer III AG, Matthews BW. Interactive graphics return to protein science. Protein Science: A Publication of the Protein Society. 2009 Mar 20;18(4):677.]

<ref group="xtra">PMID: 19461848</ref><references group="xtra" />
<blockquote>
<span style="background-color:#fffce0;">Interactivity allows a reader unbounded scope to explore a structure, taking advantage of whatever features the visualization software may provide. This is the basis underlying FirstGlance in Jmol, a service that an increasing number of journals link to, which provides standard buttons to view different aspects of a protein structure ....</span>
</blockquote>

<ref group="xtra">PMID: 21638687</ref><references group="xtra" />
<blockquote>
<span style="background-color:#fffce0;">Herráez said "I express my gratitude to Prof. Eric Martz (University of Massachusetts), long-time advocate of molecular modeling teaching, provider of Rasmol and Chime information and support on his website, of teaching-oriented recommendations and sample materials, of the excellent Protein Explorer software for macromolecule visualization and analysis, and of other countless contributions, including the recent FirstGlance in Jmol."</span>
</blockquote>

==={{Font color|#00b000|BioMedical Research}}===
<span style="background-color:#ffe0e0;">[[#Coverage|Partial Coverage]]</span>

<ref group="xtra">PMID: 20634950</ref><references group="xtra" />
<blockquote>
<span style="background-color:#fffce0;">''FirstGlance in Jmol'' was used to visualize patterns of '''evolutionary conservation''' calculated by the [http://consurf.tau.ac.il ConSurf Server].</span>
</blockquote>

<ref group="xtra">PMID: 21029378</ref><references group="xtra" />

<ref group="xtra">PMID: 18971256</ref><references group="xtra" />

<ref group="xtra">PMID: 19329630</ref><references group="xtra" />

<ref group="xtra">PMID: 19233205</ref><references group="xtra" />

* [https://books.google.com/books?hl=en&lr=&id=3jq1kSKcvEAC&oi=fnd&pg=PR11&dq=firstglance&ots=XchA-jpK7C&sig=TKhk00SK4YHR3QtLqXZU23d0jK8 Courey AJ. Mechanisms in transcriptional regulation. John Wiley & Sons; 2009 Jan 22.]
<blockquote>
<span style="background-color:#fffce0;">"''FirstGlance in Jmol'': This free program, also developed by Eric Martz, is probably '''the easiest way to look at macromolecules'''."</span>
</blockquote>

<ref group="xtra">PMID: 18067320</ref><references group="xtra" />
<blockquote>
<span style="background-color:#fffce0;">"The "'''contact residues'''" of the SH3 domain with the ligand were assigned by means of the FirstGlance in Jmol program ...."</span>
</blockquote>

<ref group="xtra">PMID: 19081051</ref><references group="xtra" />

<ref group="xtra">PMID: 18347046</ref><references group="xtra" />

==Journals Cited==

Peer-reviewed scientific papers listed above that cite ''FirstGlance in Jmol'' were published in numerous journals, including
===Education Journals===
''Biochemistry and Molecular Biology Education (8), Journal of Chemical Education.''

===Basic Research Journals===
''ACS Chemical Biology, Archives of Biophysics & Biochemistry, Biochemistry (3), BMC Microbiology, Cell Reports, Current Opinion in Virology, European Journal of Cell Biology, FEBS Journal, Gene, Journal of Cell Science, Journal of Bacteriology (2), Journal of Biological Chemistry, Journal of Molecular Biology, Molecular Microbiology, Nature Methods, Nucleic Acids Research (2), Planta, Plant Growth Regulation, Plant Cell Reports, PLOS One (9), Protein Science (3), Structure*, Scientific Reports, Trends in Biochemical Sciences (2), Veterinary Journal''.

<nowiki>*</nowiki> Nimrod ''et al.'', 2008.

===Medical Journals===
''Annals of Neurology, Infection & Immunity, Leukemia, Medical Microbiology & Immunology, PLOS Neglected Tropical Diseases.''

==References==
<references />

Salt bridges

2026-07-07T19:14:46Z

Eric Martz:

<StructureSection load='' size='300' side='right' caption='Salt bridge between retinoic acid(-) and arg131(+) in [[1cbr]].' scene='Salt_bridges/Salt_bridge/2'>

In proteins, salt bridges<ref>PMID: 21287621</ref> occur between amino acid side-chains with opposite positive or negative full-electron charges, namely, (at neutral pH) Glu- or Asp- vs. Arg+ or Lys+. They may also occur between ionized organic ligands, such as acetylcholine+ (or example at right: [[1cbr]]), or inorganic ions, such as K<sup>+</sup> or SO<sub>4</sub><sup>=</sup>, and amino acid side-chains.

A salt bridge is generally considered to exist when a nitrogen-oxygen atom pair in sidechains of (Arg,Lys)-(Asp,Glu) are ≤ 4.0 Å apart<ref name='KN2002'>PMID: 12202384</ref>.  The charged atoms could also be the amino-termini or carboxy-termini of protein chains or within non-protein ligands. The energetic significance of such complementary charge pairs is a complex function of the local environment<ref name='KN2002' />.

Proteins from [[extremophiles|thermophiles]] have more salt bridges than do proteins from mesophiles<ref>PMID:19164280</ref><ref>PMID: 11793224</ref><ref name="kumar">PMID: 11577980</ref>. These additional salt bridges contribute to stability, resisting denaturation by high temperature<ref>PMID: 21720566</ref><ref>PMID: 31360001</ref>.

==Examples==

===Thermophile vs. mesophile===
Glutamate dehydrogenase structures have been determined at about 2 Å resolution for both a thermophile, ''Pyrococcus furiosus'' ([[1gtm]]), and a mesophile, ''Clostridium symbiosum'' ([[1hrd]])<ref name="kumar" />. The thermophile's protein has 1.7 fold more N and O atoms engaged in salt bridges than does the protein from the mesophile (301 vs. 175 respectively, as counted by [[FirstGlance]]). Many of the extra salt bridges in the thermophilic enzyme cluster around the active site<ref name="kumar2000">PMID:10707024</ref>.

===Ultraviolet-B receptor===
UVR8 is an ultraviolet-B receptor in plants such as ''Arabidopsis''. It is a homodimer that, upon irradiation, dissociates into a monomer involved in transcriptional activation of UV protective proteins<ref>PMID:22388820</ref>. Unexpectedly, high ionic strength was found to dissociate the dimer. The homodimer [[4dnw]] contains many [[salt bridges]] and [[cation-pi interactions]] at the interface. [[Suggestions_for_new_articles#April:_Ultraviolet-B_Photoreceptor_Dimer_to_Monomer|More]].

===Chains and clumps of salt bridges===
[[6nie]] contains a chain of salt bridges: D236-K170-D140-R237-E120-K301. The chain branches at R237 which is salt bridged to D119. A branched chain could be described as a "clump". (K301 is an unusual monomeric amino acid ligand.)

</StructureSection>

==Visualization==

Putative protein-protein salt bridges involving charged amino acid sidechains and/or charged chain termini can be displayed by [[FirstGlance in Jmol]]. Salt bridges to ligands can be visualized using the <i>Contacts & Non-covalent interactions</i> tool, after selecting the ligand as the target for the display. Such a case is illustrated above in JSmol.

==References==
<references />

Salt bridges

2026-07-07T19:13:27Z

Eric Martz:

<StructureSection load='' size='300' side='right' caption='Salt bridge between retinoic acid(-) and arg131(+) in [[1cbr]].' scene='Salt_bridges/Salt_bridge/2'>

In proteins, salt bridges<ref>PMID: 21287621</ref> occur between amino acid side-chains with opposite positive or negative full-electron charges, namely, (at neutral pH) Glu- or Asp- vs. Arg+ or Lys+. They may also occur between ionized organic ligands, such as acetylcholine+ (or example at right: [[1cbr]]), or inorganic ions, such as K<sup>+</sup> or SO<sub>4</sub><sup>=</sup>, and amino acid side-chains.

A salt bridge is generally considered to exist when a nitrogen-oxygen atom pair in sidechains of (Arg,Lys)-(Asp,Glu) are ≤ 4.0 Å apart<ref name='KN2002'>PMID: 12202384</ref>.  The charged atoms could also be the amino-termini or carboxy-termini of protein chains. The energetic significance of such complementary charge pairs is a complex function of the local environment<ref name='KN2002' />.

Proteins from [[extremophiles|thermophiles]] have more salt bridges than do proteins from mesophiles<ref>PMID:19164280</ref><ref>PMID: 11793224</ref><ref name="kumar">PMID: 11577980</ref>. These additional salt bridges contribute to stability, resisting denaturation by high temperature<ref>PMID: 21720566</ref><ref>PMID: 31360001</ref>.

==Examples==

===Thermophile vs. mesophile===
Glutamate dehydrogenase structures have been determined at about 2 Å resolution for both a thermophile, ''Pyrococcus furiosus'' ([[1gtm]]), and a mesophile, ''Clostridium symbiosum'' ([[1hrd]])<ref name="kumar" />. The thermophile's protein has 1.7 fold more N and O atoms engaged in salt bridges than does the protein from the mesophile (301 vs. 175 respectively, as counted by [[FirstGlance]]). Many of the extra salt bridges in the thermophilic enzyme cluster around the active site<ref name="kumar2000">PMID:10707024</ref>.

===Ultraviolet-B receptor===
UVR8 is an ultraviolet-B receptor in plants such as ''Arabidopsis''. It is a homodimer that, upon irradiation, dissociates into a monomer involved in transcriptional activation of UV protective proteins<ref>PMID:22388820</ref>. Unexpectedly, high ionic strength was found to dissociate the dimer. The homodimer [[4dnw]] contains many [[salt bridges]] and [[cation-pi interactions]] at the interface. [[Suggestions_for_new_articles#April:_Ultraviolet-B_Photoreceptor_Dimer_to_Monomer|More]].

===Chains and clumps of salt bridges===
[[6nie]] contains a chain of salt bridges: D236-K170-D140-R237-E120-K301. The chain branches at R237 which is salt bridged to D119. A branched chain could be described as a "clump". (K301 is an unusual monomeric amino acid ligand.)

</StructureSection>

==Visualization==

Putative protein-protein salt bridges involving charged amino acid sidechains and/or charged chain termini can be displayed by [[FirstGlance in Jmol]]. Salt bridges to ligands can be visualized using the <i>Contacts & Non-covalent interactions</i> tool, after selecting the ligand as the target for the display. Such a case is illustrated above in JSmol.

==References==
<references />

Salt bridges

2026-07-07T19:09:32Z

Eric Martz:

<StructureSection load='' size='300' side='right' caption='Salt bridge between retinoic acid(-) and arg131(+) in [[1cbr]].' scene='Salt_bridges/Salt_bridge/2'>

In proteins, salt bridges<ref>PMID: 21287621</ref> occur between amino acid side-chains with opposite positive or negative full-electron charges, namely, (at neutral pH) Glu- or Asp- vs. Arg+ or Lys+. They may also occur between ionized organic ligands, such as acetylcholine+ (or example at right: [[1cbr]]), or inorganic ions, such as K<sup>+</sup> or SO<sub>4</sub><sup>=</sup>, and amino acid side-chains.

A salt bridge is generally considered to exist when a nitrogen-oxygen atom pair in sidechains of (Arg,Lys)-(Asp,Glu) are ≤ 4.0 Å apart<ref name='KN2002'>PMID: 12202384</ref>.  The nitrogen cation could also be the amino-terminus of a protein chain. The energetic significance of such complementary charge pairs is a complex function of the local environment<ref name='KN2002' />.

Proteins from [[extremophiles|thermophiles]] have more salt bridges than do proteins from mesophiles<ref>PMID:19164280</ref><ref>PMID: 11793224</ref><ref name="kumar">PMID: 11577980</ref>. These additional salt bridges contribute to stability, resisting denaturation by high temperature<ref>PMID: 21720566</ref><ref>PMID: 31360001</ref>.

==Examples==

===Thermophile vs. mesophile===
Glutamate dehydrogenase structures have been determined at about 2 Å resolution for both a thermophile, ''Pyrococcus furiosus'' ([[1gtm]]), and a mesophile, ''Clostridium symbiosum'' ([[1hrd]])<ref name="kumar" />. The thermophile's protein has 1.7 fold more N and O atoms engaged in salt bridges than does the protein from the mesophile (301 vs. 175 respectively, as counted by [[FirstGlance]]). Many of the extra salt bridges in the thermophilic enzyme cluster around the active site<ref name="kumar2000">PMID:10707024</ref>.

===Ultraviolet-B receptor===
UVR8 is an ultraviolet-B receptor in plants such as ''Arabidopsis''. It is a homodimer that, upon irradiation, dissociates into a monomer involved in transcriptional activation of UV protective proteins<ref>PMID:22388820</ref>. Unexpectedly, high ionic strength was found to dissociate the dimer. The homodimer [[4dnw]] contains many [[salt bridges]] and [[cation-pi interactions]] at the interface. [[Suggestions_for_new_articles#April:_Ultraviolet-B_Photoreceptor_Dimer_to_Monomer|More]].

===Chains and clumps of salt bridges===
[[6nie]] contains a chain of salt bridges: D236-K170-D140-R237-E120-K301. The chain branches at R237 which is salt bridged to D119. A branched chain could be described as a "clump". (K301 is an unusual monomeric amino acid ligand.)

</StructureSection>

==Visualization==

Putative protein-protein salt bridges involving charged amino acid sidechains and/or charged chain termini can be displayed by [[FirstGlance in Jmol]]. Salt bridges to ligands can be visualized using the <i>Contacts & Non-covalent interactions</i> tool, after selecting the ligand as the target for the display. Such a case is illustrated above in JSmol.

==References==
<references />

Salt bridges

2026-07-07T19:08:24Z

Eric Martz:

<StructureSection load='' size='300' side='right' caption='Salt bridge between retinoic acid(-) and arg131(+) in [[1cbr]].' scene='Salt_bridges/Salt_bridge/2'>

In proteins, salt bridges<ref>PMID: 21287621</ref> occur between amino acid side-chains with opposite positive or negative full-electron charges, namely, (at neutral pH) Glu- or Asp- vs. Arg+ or Lys+. They may also occur between ionized organic ligands, such as acetylcholine+ (or example at right: [[1cbr]]), or inorganic ions, such as K<sup>+</sup> or SO<sub>4</sub><sup>=</sup>, and amino acid side-chains.

A salt bridge is generally considered to exist when a nitrogen-oxygen atom pair in sidechains of (Arg,Lys)-(Asp,Glu) are ≤ 4.0 Å apart<ref>PMID: 12202384</ref>.  The nitrogen cation could also be the amino-terminus of a protein chain. The energetic significance of such complementary charge pairs is a complex function of the local environment<ref name='KN2002' />.

Proteins from [[extremophiles|thermophiles]] have more salt bridges than do proteins from mesophiles<ref>PMID:19164280</ref><ref>PMID: 11793224</ref><ref name="kumar">PMID: 11577980</ref>. These additional salt bridges contribute to stability, resisting denaturation by high temperature<ref>PMID: 21720566</ref><ref>PMID: 31360001</ref>.

==Examples==

===Thermophile vs. mesophile===
Glutamate dehydrogenase structures have been determined at about 2 Å resolution for both a thermophile, ''Pyrococcus furiosus'' ([[1gtm]]), and a mesophile, ''Clostridium symbiosum'' ([[1hrd]])<ref name="kumar" />. The thermophile's protein has 1.7 fold more N and O atoms engaged in salt bridges than does the protein from the mesophile (301 vs. 175 respectively, as counted by [[FirstGlance]]). Many of the extra salt bridges in the thermophilic enzyme cluster around the active site<ref name="kumar2000">PMID:10707024</ref>.

===Ultraviolet-B receptor===
UVR8 is an ultraviolet-B receptor in plants such as ''Arabidopsis''. It is a homodimer that, upon irradiation, dissociates into a monomer involved in transcriptional activation of UV protective proteins<ref>PMID:22388820</ref>. Unexpectedly, high ionic strength was found to dissociate the dimer. The homodimer [[4dnw]] contains many [[salt bridges]] and [[cation-pi interactions]] at the interface. [[Suggestions_for_new_articles#April:_Ultraviolet-B_Photoreceptor_Dimer_to_Monomer|More]].

===Chains and clumps of salt bridges===
[[6nie]] contains a chain of salt bridges: D236-K170-D140-R237-E120-K301. The chain branches at R237 which is salt bridged to D119. A branched chain could be described as a "clump". (K301 is an unusual monomeric amino acid ligand.)

</StructureSection>

==Visualization==

Putative protein-protein salt bridges involving charged amino acid sidechains and/or charged chain termini can be displayed by [[FirstGlance in Jmol]]. Salt bridges to ligands can be visualized using the <i>Contacts & Non-covalent interactions</i> tool, after selecting the ligand as the target for the display. Such a case is illustrated above in JSmol.

==References==
<references />

Salt bridges

2026-07-07T19:06:10Z

Eric Martz:

<StructureSection load='' size='300' side='right' caption='Salt bridge between retinoic acid(-) and arg131(+) in [[1cbr]].' scene='Salt_bridges/Salt_bridge/2'>

In proteins, salt bridges<ref>PMID: 21287621</ref> occur between amino acid side-chains with opposite positive or negative full-electron charges, namely, (at neutral pH) Glu- or Asp- vs. Arg+ or Lys+. They may also occur between ionized organic ligands, such as acetylcholine+ (or example at right: [[1cbr]]), or inorganic ions, such as K<sup>+</sup> or SO<sub>4</sub><sup>=</sup>, and amino acid side-chains.

A salt bridge is generally considered to exist when a nitrogen-oxygen atom pair in sidechains of (Arg,Lys)-(Asp,Glu) are ≤ 4.0 Å apart<ref>PMID: 12202384</ref>.  The energetic significance of such complementary charge pairs is a complex function of the local environment<ref name="KN2002" />.

Proteins from [[extremophiles|thermophiles]] have more salt bridges than do proteins from mesophiles<ref>PMID:19164280</ref><ref>PMID: 11793224</ref><ref name="kumar">PMID: 11577980</ref>. These additional salt bridges contribute to stability, resisting denaturation by high temperature<ref>PMID: 21720566</ref><ref>PMID: 31360001</ref>.

==Examples==

===Thermophile vs. mesophile===
Glutamate dehydrogenase structures have been determined at about 2 Å resolution for both a thermophile, ''Pyrococcus furiosus'' ([[1gtm]]), and a mesophile, ''Clostridium symbiosum'' ([[1hrd]])<ref name="kumar" />. The thermophile's protein has 1.7 fold more N and O atoms engaged in salt bridges than does the protein from the mesophile (301 vs. 175 respectively, as counted by [[FirstGlance]]). Many of the extra salt bridges in the thermophilic enzyme cluster around the active site<ref name="kumar2000">PMID:10707024</ref>.

===Ultraviolet-B receptor===
UVR8 is an ultraviolet-B receptor in plants such as ''Arabidopsis''. It is a homodimer that, upon irradiation, dissociates into a monomer involved in transcriptional activation of UV protective proteins<ref>PMID:22388820</ref>. Unexpectedly, high ionic strength was found to dissociate the dimer. The homodimer [[4dnw]] contains many [[salt bridges]] and [[cation-pi interactions]] at the interface. [[Suggestions_for_new_articles#April:_Ultraviolet-B_Photoreceptor_Dimer_to_Monomer|More]].

===Chains and clumps of salt bridges===
[[6nie]] contains a chain of salt bridges: D236-K170-D140-R237-E120-K301. The chain branches at R237 which is salt bridged to D119. A branched chain could be described as a "clump". (K301 is an unusual monomeric amino acid ligand.)

</StructureSection>

==Visualization==

Putative protein-protein salt bridges involving charged amino acid sidechains and/or charged chain termini can be displayed by [[FirstGlance in Jmol]]. Salt bridges to ligands can be visualized using the <i>Contacts & Non-covalent interactions</i> tool, after selecting the ligand as the target for the display. Such a case is illustrated above in JSmol.

==References==
<references />

Cation Pi Interactions

2026-06-08T18:21:05Z

Eric Martz: Changed redirect target from Cation pi interactions to Cation-pi interactions

#REDIRECT [[Cation-pi interactions]]

Cation Pi Interactions

2026-06-08T18:17:41Z

Eric Martz: Redirected page to Cation pi interactions

#REDIRECT [[Cation pi interactions]]