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:Team]]
** [[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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**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]]
*''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]
*[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]
*[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 usful views. This 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/pe_beta/pe/protexpl/igloss.htm Protein Explorer's Glossary]
*[http://www.umass.edu/microbio/chime/pe_beta/pe/protexpl/igloss.htm Protein Explorer's Glossary]
*[http://www.bioinformatics.org/jmol-tutorials/jtat/_docs/jmol_app.htm Jmol Application]
*[http://www.bioinformatics.org/jmol-tutorials/jtat/_docs/jmol_app.htm Jmol Application]
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*[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.weizmann.ac.il/ISPC/eMovie.html eMovie],a [http://pymol.org/ PyMol] plug-in for macromolecular movie-making.
*[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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*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.
*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].
*[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]
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