User:Wayne Decatur/UNH Seminar Feb 1st 2011: Difference between revisions
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**Cursory coverage of several free (and mainly open-source) options for molecular visualization | **Cursory coverage of several free (and mainly open-source) options for molecular visualization | ||
*[http://www.pymolwiki.org/index.php/Mutagenesis Mutagenesis using PyMOL]. Similar approach can be done in Swiss-PDB Viewer (a.k.a. DeepView). | |||
==Yeast snoRNAs== | ==Yeast snoRNAs== | ||
*Introduction to snoRNAs - most modify and are not-essential to yeast | *Introduction to snoRNAs - most modify and are not-essential to yeast | ||
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==Proteopedia== | ==Proteopedia== | ||
*[[Main Page|Proteopedia]] - interactive 3D encylopedia of macromolecular structures and structural biology resources to which scientists contribute and use to share structural biology content | *[[Main Page|Proteopedia]] - interactive 3D encylopedia of macromolecular structures and structural biology resources to which scientists contribute and use to share structural biology content | ||
*People behind Proteopedia | *People behind Proteopedia | ||
** [[Proteopedia:Team]] | |||
**Users, like You! | **Users, like You! | ||
*[[Help:Getting Started in Proteopedia]] | |||
==Types of Proteopedia pages== | ==Types of Proteopedia pages== | ||
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*PDB Entry Pages | *PDB Entry Pages | ||
*User space Pages | *User space Pages | ||
*Sandbox Pages | *Sandbox Pages -->, see [[Help:Sandboxes]] | ||
*Workbench Pages | *Workbench Pages | ||
*Interactive 3D Complements (I3DC) - [[Journal of Biological Inorganic Chemistry]] | *Interactive 3D Complements (I3DC) - [[Journal of Biological Inorganic Chemistry]] | ||
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***Quality toggle | ***Quality toggle | ||
***Popup | ***Popup | ||
**[[Citrate | **[[Citrate Synthase]] | ||
**[[Glutamate receptor (GluA2)|The Glutamate Receptor (GluA2)]] | **[[Glutamate receptor (GluA2)|The Glutamate Receptor (GluA2)]] | ||
***Proteopedia pages can be exported for offline viewing using the toolbox on the left. | ***Proteopedia pages can be exported for offline viewing using the toolbox on the left. | ||
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==PDB Entry Pages== | ==PDB Entry Pages== | ||
*Proteopedia has an entry for every PDB entry (over 70,000) with interactive scene links and links to useful | *Proteopedia has an entry for every PDB entry (over 70,000) with interactive scene links and links to useful resources | ||
** Example [[1m10]] | ** Example [[1m10]] | ||
**Random Example: [[1p3v]] (PDB 4 digit alphanumeric accession number) | **Random Example: [[1p3v]] (PDB 4 digit alphanumeric accession number) | ||
***Conservation: , explanation, and see also [http://consurfdb.tau.ac.il/comparison.php The ConSurf Database] and [http://consurf.tau.ac.il/ The ConSurf Server] | ***Conservation: , explanation, and see also [http://consurfdb.tau.ac.il/comparison.php The ConSurf Database] and [http://consurf.tau.ac.il/ The ConSurf Server] Other examples: [[4enl]] or [[5cyt]] | ||
==FirstGlance in Jmol== | ==FirstGlance in Jmol== | ||
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**Buttons for 3D structure windows and other commonly used items | **Buttons for 3D structure windows and other commonly used items | ||
**Since a large amount of references are from Pub-Med, PMID all that is needed for references | **Since a large amount of references are from Pub-Med, PMID all that is needed for references | ||
*[[Help:Getting Started in Proteopedia]] | |||
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===Macromolecular Visualization=== | ===Macromolecular Visualization=== | ||
*[http://www.umass.edu/molvis/workshop/umass11.htm Eric Martz's recent workshop] at [http://workshops.molviz.org his list of workshops]. | *[http://www.umass.edu/molvis/workshop/umass11.htm Eric Martz's recent workshop] at [http://workshops.molviz.org 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. [http://genomebiology.com/2008/9/8/R121 ''Genome Biology'' 9:R121, August 2008] or [http://dx.doi.org/10.1186/gb-2008-9-8-r121 doi:10.1186/gb-2008-9-8-r121] | |||
*[[About Macromolecular Structure]] | *[[About Macromolecular Structure]] | ||
* | *[http://molvis.sdsc.edu/fgij/ FirstGlance in Jmol] is very useful for exploring PDB entries or upload structure files. | ||
*[http://chemapps.stolaf.edu/pe/protexpl/ 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. | |||
*[http://www.umass.edu/microbio/chime/top5.htm MolviZ "Top 5"] | *[http://www.umass.edu/microbio/chime/top5.htm MolviZ "Top 5"] | ||
*[http://www.umass.edu/microbio/chime/index.html MolviZ.Org] | *[http://www.umass.edu/microbio/chime/index.html MolviZ.Org] | ||
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*[http://pymol.org/ PyMol] | *[http://pymol.org/ PyMol] | ||
*[http://polyview.cchmc.org/polyview3d.html Polyview-3D], fancy [http://pymol.org/ PyMol] views and animations made super easy via a web server with forms. | *[http://polyview.cchmc.org/polyview3d.html Polyview-3D], fancy [http://pymol.org/ PyMol] views and animations made super easy via a web server with forms. | ||
*[http:// | *[http://www.weizmann.ac.il/ISPC/eMovie.html eMovie],a [http://pymol.org/ PyMol] plug-in for macromolecular movie-making. | ||
===Small Molecule Visualization and Model Kits=== | ===Small Molecule Visualization and Model Kits=== | ||
*[http://chemagic.com/web_molecules/script_page_large.aspx CheMagic Virtual Molecular Model Kit] | *[http://chemagic.com/web_molecules/script_page_large.aspx CheMagic Virtual Molecular Model Kit] | ||
*[http://butane.chem.illinois.edu/jsmoore/Experimental/mpjmols/JManip.aspx The Jmol Interface by Mike Evans at University of Illinois] has a model kit interface and easy ways to arrows and items. | |||
*[http://chemcanvas.sourceforge.net/chemWin.html ChemCanvas, an open source chemical diagram editor] | *[http://chemcanvas.sourceforge.net/chemWin.html ChemCanvas, an open source chemical diagram editor] | ||
*[http://www.chemtube3d.com/index.html ChemTube3D] has interactive animations and structures of molecules and reactions important in chemistry. | *[http://www.chemtube3d.com/index.html ChemTube3D] has interactive animations and structures of molecules and reactions important in chemistry. | ||
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===Authoring Scenes and Views in Proteopedia and beyond=== | ===Authoring Scenes and Views in Proteopedia and beyond=== | ||
*[[Help:Getting Started in Proteopedia]] | |||
*[[Proteopedia:Video Guide]] | *[[Proteopedia:Video Guide]] | ||
* [[Proteopedia:How to Make a Page]] | * [[Proteopedia:How to Make a Page]] | ||
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*[http://chemapps.stolaf.edu/pe/protexpl/ Jmol Protein Explorer's] powerful Quickviews approach really helps quickly generate particular scenes or ideas for scenes to generate elsewhere. Using the information detailed [[Help:Copying FirstGlance Scenes into Proteopedia|here]] or at [http://www.bioinformatics.org/jmol-tutorials/jtat/_docs/jtatdocs.htm#fgijscripting 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. | *[http://chemapps.stolaf.edu/pe/protexpl/ Jmol Protein Explorer's] powerful Quickviews approach really helps quickly generate particular scenes or ideas for scenes to generate elsewhere. Using the information detailed [[Help:Copying FirstGlance Scenes into Proteopedia|here]] or at [http://www.bioinformatics.org/jmol-tutorials/jtat/_docs/jtatdocs.htm#fgijscripting 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. | ||
*[http://www.bioinformatics.org/jmol-tutorials/jtat/_docs/index.htm Jmol Tutorial-Authoring Template (JTAT)] describes and works for developing and viewing scenes offline or developing and viewing privately. | *[http://www.bioinformatics.org/jmol-tutorials/jtat/_docs/index.htm Jmol Tutorial-Authoring Template (JTAT)] describes and works for developing and viewing scenes offline or developing and viewing privately. | ||
*[http://chemapps.stolaf.edu/jmol/docs/ Jmol Command Reference Manual] for advanced scene authoring. | |||
*[http://wiki.jmol.org/index.php?title=Main_Page Jmol Wiki] | |||
*[[Morphs|Morphing]] allows displaying the visual transition between two molecular conformations. | *[[Morphs|Morphing]] allows displaying the visual transition between two molecular conformations. | ||
*[http://polyview.cchmc.org/polyview3d.html Polyview-3D], fancy [http://pymol.org/ PyMol] views and animations made super easy via a web server with forms. | *[http://polyview.cchmc.org/polyview3d.html Polyview-3D], fancy [http://pymol.org/ PyMol] views and animations made super easy via a web server with forms. | ||
*[http://www. | |||
===Modeling=== | |||
*See the end of [http://www.umass.edu/molvis/workshop/umass11.htm Eric Martz's recent workshop syllabus] where he covers homology (more accurately, comparative) modeling. | |||
*[http://www.biotechniques.com/news/biotechniquesNews/biotechniques-309517.html A Feb. 1st 2011 news item about Yang Zhang and his work]. | |||
* Mutating an amino acid in a proteins - [http://www.pymolwiki.org/index.php/Mutagenesis here with PyMOL] and [http://spdbv.vital-it.ch/mutation_guide.html here with Swiss PDB-Viewer] | |||
*Homology modeling | |||
**[http://www.umass.edu/molvis/workshop/homolmod.htm Eric Martz's page on Homology Modeling] | |||
**[http://swissmodel.expasy.org/ Swiss Model] | |||
**[http://skybase.c2b2.columbia.edu/nesg3/help/help.html Homology Models Database] | |||
**[http://modbase.compbio.ucsf.edu/modbase-cgi/index.cgi Modbase -Database of Comparative Protein Structure Models] | |||
*Comparative Modeling | |||
**[http://zhanglab.ccmb.med.umich.edu/I-TASSER/ Zhang Server (I-TASSER) ] | |||
*Ab Initio and Molecular Dynamics | |||
**[http://zhanglab.ccmb.med.umich.edu/QUARK/ Quark server] | |||
**[http://www.ks.uiuc.edu/Research/vmd/ VMD - Visual Molecular Dynamics] | |||
