User:Wayne Decatur/UNH Seminar Feb 1st 2011 - Revision history

Wayne Decatur at 14:21, 27 March 2012

2012-03-27T14:21:41Z

← Older revision		Revision as of 14:21, 27 March 2012
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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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	**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===
			*[[Help:Getting Started in Proteopedia]]
	*[[Proteopedia:Video Guide]]		*[[Proteopedia:Video Guide]]
	* [[Proteopedia:How to Make a Page]]		* [[Proteopedia:How to Make a Page]]

Wayne Decatur: /* Types of Proteopedia pages */

2011-05-01T01:32:28Z

Types of Proteopedia pages

← Older revision		Revision as of 01:32, 1 May 2011
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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]]

Wayne Decatur at 01:23, 11 March 2011

2011-03-11T01:23:18Z

← Older revision		Revision as of 01:23, 11 March 2011
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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]

Wayne Decatur at 21:54, 7 March 2011

2011-03-07T21:54:13Z

← Older revision		Revision as of 21:54, 7 March 2011
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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.		*[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

Wayne Decatur at 21:53, 7 March 2011

2011-03-07T21:53:51Z

← Older revision		Revision as of 21:53, 7 March 2011
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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

Wayne Decatur: /* Small Molecule Visualization and Model Kits */

2011-02-20T17:42:13Z

Small Molecule Visualization and Model Kits

← Older revision		Revision as of 17:42, 20 February 2011
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	===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.

Wayne Decatur: /* Macromolecular Visualization */

2011-02-03T16:03:00Z

Macromolecular Visualization

← Older revision		Revision as of 16:03, 3 February 2011
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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 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/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]

Wayne Decatur: /* Macromolecular Visualization */

2011-02-03T15:52:08Z

Macromolecular Visualization

← Older revision		Revision as of 15:52, 3 February 2011
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	*[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://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://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/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===

Wayne Decatur: /* Resources */

2011-02-03T15:47:33Z

Resources

← Older revision		Revision as of 15:47, 3 February 2011
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	*[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]
	*[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://~~chemapps~~.~~stolaf~~.~~edu~~/~~jmol~~/~~docs/ Jmol Command Reference Manual~~] ~~for advanced scene authoring.~~		*[http://www.weizmann.ac.il/ISPC/eMovie.html eMovie],a [http://pymol.org/ PyMol] plug-in for macromolecular movie-making.
	*[http://~~wiki.jmol~~.org/~~index~~.~~php?title=Main_Page Jmol Wiki]~~

	===Small Molecule Visualization and Model Kits===		===Small Molecule Visualization and Model Kits===
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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.~~weizmann~~.~~ac.il~~/~~ISPC~~/~~eMovie~~.~~html eMovie~~],a [http://~~pymol~~.~~org~~/ ~~PyMol~~] ~~plug-in for macromolecular movie-making~~.

			===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].

Wayne Decatur: fixed typo in citrate synthase

2011-02-01T18:07:24Z

fixed typo in citrate synthase

← Older revision		Revision as of 18:07, 1 February 2011
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	***Quality toggle		***Quality toggle
	***Popup		***Popup
	**[[Citrate ~~synthase~~]]		**[[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.