User:Wayne Decatur/NASCE2011
From Proteopedia
General Introduction
- Thanks to the organizers of the NASCE2011
- About me
- Overview of the workshop planned
- Gauge Audience, Adjust plan?
Introduction to Proteopedia
- Main Page
- Sightseeing by way of example "Case Studies" / "User Narratives"
- Topics
- main page--->Ribosome structure, spin, hover, measure distances, toggles, list, contributors --->page particular section ---> another page green links
- via search---> The Glutamate Receptor (GluA2) quality, popup, section window
- Open-ended Gateway
- learn of a structure in a meeting (Robert Milllar talk on Saturday) ---> Pubmed search result---> 2rh1
- Sites
- ConSurf
- Firstglance in Jmol
- new publication ---> 3rze Sites
- note where link to 3D structure at Nature publication goes
- learn of a structure in a meeting (Robert Milllar talk on Saturday) ---> Pubmed search result---> 2rh1
- Student aid - Proteopedia:Table of Contents -->Metabolism -->Carbohydrate Metabolism -->Citric Acid Cycle--> Citrate Synthase morphs and reaction steps in second section
- Lecturing
- User:Eric Martz/Nucleosomes
- resources for this workshop as listed under Workshops and Seminars on my user page as Workshop for the NASCE Meeting at the University of Michigan, Ann Arbor, MI July 13 2011
- Structural Biology Resource
- Student Projects
- Journal Club --> RecG Bound to Three-Way DNA Junction
- Communicating specific ideas in context of structure --> e-mail a link to a Sandbox, e.g. Sandbox CsrA
- Group meeting ---> Proteopedia:Workbench, also good for preparing for publication
- Publications
- Topics
Under the Hood
- Wiki implementation, very specialized
- references
- Create a page for example with references
- other technical aspects related to Jmol and other media
- references
- Jmol
Jmol
- Jmol
- The Application
- The Java Applet - Demonstration with Human Follicle-Stimulating Hormone Complexed with its Receptor
- Advanced Options
- Console
- Compare Command Demonstration
- Sculpting - Simple example of that here
- 3D options - Demo with Hormone
The Structure Data
- everything centers around an Atomic coordinate file
- Experimental vs theoretical sources
Protein Data Bank
- nearly 75,000 X-ray crystallography, NMR, and cryo-EM structures
- PDB statistics
- about 85% are crystallographic structures - hydrogens anyone? Hydrogen in macromolecular models
- Isomesh of electron density helps illustrate how crystallographic models get built using a portion of one
- Caveat: Keep in mind these are models - Not all models created equally
- one gauge Resolution noted with a link on each PDB entry page
Proteopedia
- Proteopedia - interactive 3D encylopedia of macromolecular structures and structural biology resources to which scientists contribute and use to share structural biology content
- Help:Getting Started in Proteopedia
- User or Sandbox login
- We encourage you all to become users of any sort. If you become a registered user, you can save information in your userspace regardless of your overall contribution to public spaces.
Types of Proteopedia pages
- Topic Pages
- Macromolecular Structures
- About Macromolecular Structure
- PDB Entry Pages
- User space Pages
- Sandbox Pages , see Help:Sandboxes
- Workbench Pages ,see Proteopedia:Workbench and Group:SMART:Workbench_SMART_Teams#
- Interactive 3D Complements (I3DC) - Journal of Biological Inorganic Chemistry
- Administrative
- How To/Guides
- Organizational/Table of Contents
- Main Page - the main gateway
Topic Pages
- Additional examples of topic pages concerning structures
- Hemolysin
- Proteopedia pages can be exported for offline viewing using the toolbox on the left.
- Hemolysin
- Information and Resource Collection, as well
User Pages
- Other users cannot edit pages in this space
PDB Entry Pages
- Proteopedia has an entry for every PDB entry (nearly 75,000) with interactive scene links and links to useful resources
- Example 1p3v (PDB 4 digit alphanumeric accession number)
- Evolutionary conservation - conserved patches are good candidates for functional sites: see explanation and caveat, and see also The ConSurf Database and The ConSurf Server Other examples: 4enl or 5cyt
- Show how to use ConSurf Server - Be sure to choose to "Let me select the sequences for the analysis manually out of Blast results"
- Evolutionary conservation - conserved patches are good candidates for functional sites: see explanation and caveat, and see also The ConSurf Database and The ConSurf Server Other examples: 4enl or 5cyt
- Example 1p3v (PDB 4 digit alphanumeric accession number)
FirstGlance in Jmol
- Views and Convenience buttons
- How many chains? - Use 3pla
- Key Resources:
- Biological Unit
- Missing pieces?; PDBsum link on Proteopedia entry pages helpful for this as well
- Under adoptions on main page , there is Orientations of Proteins in Membranes (OPM) database from the University of Michigan (Ann Arbor, Michigan, USA), and knowing the spatial arrangement of protein with respect to the hydrocarbon core of the lipid bilayer and other details of topology could be useful for understanding the function of several proteins involved in endocrinology, example 2rh1
- Also accessible via Membrane proteins from within Proteopedia
Structural Biology for Non-structural Biologists
- MolviZ "Top 5" by Eric Martz
- Polyview-3D = fancy PyMol views and animations made super easy via a web server with forms.
- Example for 2rh1
- Use overall structure with ligands off; under chain and color rendering chain a as cartoon and hide remaining; under individual residue highlight enter a:408:cf,a:290:ms from converter
- 2rh1 from Polyview-3D (probably the gap in the cartoon is an artifact due to the way the numbering is for 2rh1 due to the chimeric nature of the receptor with lysozyme (see PDBSum
- Makes animations too and/or morphs as well using a file with multiple models
- Example for 2rh1
Proteopedia Page Authoring
- Model of a wiki
- Sandbox - there is a "student" login that can be used by groups for editing these for teaching purposes
- Conveniences
- Buttons for 3D structure windows and other commonly used items
- Since a large amount of references are from PubMed, PMID all that is needed for references in text, combined with a reference list at end
- Proteopedia:How to Make a Page
- How to edit pages in Proteopedia
- Special:Upload List of allowed file types: png, jpg, jpeg, tiff, tif, gif, mgif, pdb, cif, mmcif, cml, mol, xyz, kin, mmol
- To do:
- Try making a sandbox page
- Add a subject or title to your page
- Insert a 3D structure window on your page
Proteopedia Scene Authoring and Adding Green Scene Links to a Page
- Proteopedia's Scene Authoring Tools
- To do:
- Load a structure 3ciy or previous scene
- Set your scene. Undo/Redo features.
- Save your scene
- Try it out and then add and improve. Repeat until you are happy with result.
- Add the scene to the page you made by pasting the text from the scene text box into the page editing box.
- Return to scene authoring tools to make more scenes or improve the one you have.
- If you update a scene, change the text on the page to designate playing of the new scene.
Time or need permitting
- Advanced scenes/toggles - Human Follicle-Stimulating Hormone Complexed with its Receptor has several examples
- Morphing allows displaying the visual transition between two molecular conformations.
- Pymol to Jmol conversion built into Proteopedia's Scene Authoring Tools
- Jmol works with small molecules too
- Works with small molecules too and even can do energy minimization with them
- Can be used to show chemical reactions
- Recalling the Caveat: Keep in mind these are models -Not only are not all models models created equally, not even all portions of models are created equally
- Assessing structure
- Resolution noted with a link on each PDB entry page
- Temperature factors, also see demonstration here
- Gaps, i.e. missing pieces (see above)
- Can't find an empirical 3D model for your sequence?
- Use the sequence of your protein to search the Structural Genomics Target Database for crystal structures nearing publication.
- Endeavor to generate a theoretical model by one of various means
Resources
Macromolecular Visualization
- Eric Martz's recent workshop at his list of workshops.
- Proteopedia - a scientific 'wiki' bridging the rift between 3D structure and function of biomacromolecules, Eran Hodis, Jaime Prilusky, Eric Martz, Israel Silman, John Moult and Joel L Sussman. Genome Biology 9:R121, August 2008 or doi:10.1186/gb-2008-9-8-r121
- About Macromolecular Structure
- FirstGlance in Jmol is very useful for exploring PDB entries or upload structure files.
- Easily compare the size of macromolecules easily with this page. It works on any device because it has both a Java-based and javascript-based option.
- Jmol Protein Explorer's powerful Quickviews approach really helps quickly generate useful views. This effort is building Chime-based Protein Explorer to work with Jmol, and a few features may still not yet work.
- MolviZ "Top 5"
- MolviZ.Org
- Protein Explorer's Glossary
- Jmol Application
- PyMol
- Polyview-3D, fancy PyMol views and animations made super easy via a web server with forms.
- eMovie,a PyMol plug-in for macromolecular movie-making.
Small Molecule Visualization and Model Kits
- CheMagic Virtual Molecular Model Kit that works on most any device!! - Uses JSmol
- JSME Molecular Editor - , the non-Java alternative to JME; uses JSmol [1]
- CheMagic Virtual Molecular Model Kit - Java based so only works on computers
- The Jmol Interface by Mike Evans at University of Illinois has a model kit interface and easy ways to arrows and items.
- ChemCanvas, an open source chemical diagram editor
- ChemTube3D has interactive animations and structures of molecules and reactions important in chemistry.
- Service allowing young people to look up a molecule and blow it up and put it back together
- ChemDoodleWeb Integrated with Jmol
- Scribmol is a ChemDoodleWeb Integrated with Jmol application found at a utilities page (french) with other useful visualization tools.
- CheS-Mapper (Chemical Space Mapper) is a 3D-viewer for chemical datasets with small compounds. It on the fly divides large datasets into clusters of similar compounds, arranging them in 3D space, such that their spatial proximity reflects their similarity. It is an open-source Java application, based on the Java libraries Jmol, CDK, WEKA, and utilizes OpenBabel and R.
Topic Pages - Education
Authoring Scenes and Views in Proteopedia and beyond
- Proteopedia:Video Guide
- Help:Getting Started in Proteopedia
- Proteopedia:How to Make a Page
- How to edit pages in Proteopedia ? Example 1, example 2, and example 3 of edited topic pages.
- Special:Upload List of allowed file types: png, jpg, jpeg, tiff, tif, gif, mgif, pdb, cif, mmcif, cml, mol, xyz, kin, mmol
- Proteopedia's Scene Authoring Tools
- Perform basic editing and creation of scenes in your Sandboxes
- Copying FirstGlance Scenes into Proteopedia
- User:Tom Gluick/glutamine synthetase (University of Maryland, Baltimore County). Includes instructions for using Jmol commands in the Jmol console for advanced scene authoring.
- Jmol Command Reference Manual for advanced scene authoring in Jmol using commands because direct scripting works for Proteopedia too.
- Comparison of Jmol tutorial-authoring systems
- Copying FirstGlance in Jmol Scenes into Proteopedia
- Jmol Protein Explorer's powerful Quickviews approach really helps quickly generate particular scenes or ideas for scenes to generate elsewhere. Using the information detailed here or at the JTAT site on extracting state scripts, it is possible to go from these views to Proteopedia scenes; however, as the version of Jmol differs there may be discrepancies and issues.
- Jmol Tutorial-Authoring Template (JTAT) describes and works for developing and viewing scenes offline or developing and viewing privately.
- Jmol Command Reference Manual for advanced scene authoring.
- Jmol Wiki
- Morphing allows displaying the visual transition between two molecular conformations.
- Polyview-3D, fancy PyMol views and animations made super easy via a web server with forms.
Modeling
- See the end of Eric Martz's recent workshop syllabus where he covers homology (more accurately, comparative) modeling.
- A Feb. 1st 2011 news item about Yang Zhang and his work.
- Mutating an amino acid in a protein - here with PyMOL and here with Swiss PDB-Viewer
- Homology modeling
- Comparative Modeling
- Ab Initio and Molecular Dynamics
- RNA modeling
- Secondary Structure
- The methods page for CompaRNA lists and provides links to several software and server-based programs for secondary structure prediction.
- NASP is a parallel program for identifying evolutionarily conserved nucleic acid secondary structures from nucleotide sequence alignments. See the companion article.
- 3D Structure
- ModeRNA server is an online tool for RNA 3D structure modeling by the comparative approach, based on a template RNA structure and a user-defined target-template sequence alignment. Related to this is ModeRNA ModeRNA, which is a program for comparative modeling of RNA 3D structures. It requires a pairwise sequence alignment and a structural template to generate a 3D structural model of the target RNA sequence and allows for nucleotide modifications. See the companion article for the server.
- Secondary Structure
- RNA-protein modeling
- The software page at the Bujnicki Laboratory website hosts software for determining two medium-resolution, knowledge-based potentials for scoring protein-RNA models obtained by docking. See the companion article.
References
- ↑ B. Bienfait and P. Ertl, JSME: a free molecule editor in JavaScript, Journal of Cheminformatics 5:24 (2013) article
