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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===Authoring Scenes and Views in Proteopedia and beyond=== | ===Authoring Scenes and Views in Proteopedia and beyond=== | ||
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*[[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] | |||
