User:Wayne Decatur/NASCE2011: Difference between revisions

(19 intermediate revisions by the same user not shown)

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* nearly 75,000 X-ray crystallography, NMR, and cryo-EM structures

* [http://www.pdb.org/pdb/statistics/contentGrowthChart.do?content=total&seqid=100 PDB statistics]

* about 85% are crystallographic structures

* about 85% are crystallographic structures - hydrogens anyone? [[Hydrogen in macromolecular models]]

*[http://www.umass.edu/molvis/edm/cloud/index.htm 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

** one gauge [[Resolution]] noted with a link on each PDB entry page

==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

*[[Help:Getting Started in Proteopedia]]

*User or Sandbox login

*We encourage you all to become users of any sort. If you become a registered, you can save information in your userspace regardless of your overall contribution to public spaces.

*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==

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*PDB Entry Pages

*User space Pages

*Sandbox Pages

*Sandbox Pages , see [[Help:Sandboxes]]

*Workbench Pages

*Workbench Pages ,see [[Proteopedia:Workbench]] and [[Group:SMART:Workbench_SMART_Teams#]]

*Interactive 3D Complements (I3DC) - [[Journal of Biological Inorganic Chemistry]]

*Administrative

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***Biological Unit

***Missing pieces?; PDBsum link on Proteopedia entry pages helpful for this as well

*Under adoptions on [http://molvis.sdsc.edu/fgij/index.htm main page] , there is [http://opm.phar.umich.edu/ Orientations of Proteins in Membranes (OPM) database] from the University of Michigan (Ann Arbor, Michigan, USA), ~~which~~ could be useful for several proteins involved in endocrinology, example [[2rh1]]

*Under adoptions on [http://molvis.sdsc.edu/fgij/index.htm main page] , there is [http://opm.phar.umich.edu/ 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

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* [[Proteopedia:How to Make a Page]]

*[[Help:Editing|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==

==Proteopedia Scene Authoring and Adding Green Scene Links to a Page==

*[[Scene authoring tools|Proteopedia's Scene Authoring Tools]]

*To do:

**Load a structure [[3ciy]] or previous scene

**Set your scene. Undo/Redo features.

**Save your scene

*Save your scene

**Add the scene to the page

**Try it out and then add and improve. Repeat until you are happy with result.

*~~Try it out and then add and~~ improve. ~~Repeat~~.

*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.

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*[[About Macromolecular Structure]]

*[http://molvis.sdsc.edu/fgij/ FirstGlance in Jmol] is very useful for exploring PDB entries or upload structure files.

*[http://biomodel.uah.es/en/scale/ 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.

*[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"]

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===Small Molecule Visualization and Model Kits===

*[http://chemagic.com/web_molecules/script_page_large.aspx CheMagic Virtual Molecular Model Kit]

*[http://chemagic.com/draw.htm CheMagic Virtual Molecular Model Kit that works on most any device!!] - Uses JSmol

*[http://biomodel.uah.es/en/DIY/JSME/ JSME Molecular Editor] - , the non-Java alternative to JME; uses JSmol <ref>B. Bienfait and P. Ertl, JSME: a free molecule editor in JavaScript, Journal of Cheminformatics 5:24 (2013) [http://www.jcheminf.com/content/5/1/24 article]</ref>

*[http://chemagic.com/web_molecules/script_page_large.aspx CheMagic Virtual Molecular Model Kit] - Java based so only works on computers

*[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://www.chemtube3d.com/index.html ChemTube3D] has interactive animations and structures of molecules and reactions important in chemistry.

*[http://chemagic.com/web_molecules/acs.aspx Service allowing young people to look up a molecule and blow it up and put it back together]

*[http://chemapps.stolaf.edu/jmol/docs/examples-12/ChemDoodleWeb/samples/sketcher_Jmol.html ChemDoodleWeb Integrated with Jmol]

*[http://librairiedemolecules.education.fr/outils/scribmol/ Scribmol] is a ChemDoodleWeb Integrated with Jmol application found at [http://librairiedemolecules.education.fr/outils/ a utilities page] (french) with other useful visualization tools.

* [http://opentox.informatik.uni-freiburg.de/ches-mapper/ 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===

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===Authoring Scenes and Views in Proteopedia and beyond===

*[[Proteopedia:Video Guide]]

* [[Help:Getting Started in Proteopedia]]

* [[Proteopedia:How to Make a Page]]

*[[Help:Editing|How to edit pages in Proteopedia]] ? [[Ribosome|Example 1]], [[User:Wayne Decatur/Plant Viral Protein p19 Suppression of RNA Silencing|example 2]], and [[Avian Influenza Neuraminidase, Tamiflu and Relenza|example 3]] of edited topic pages.

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*[[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.

===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]

* Mutating an amino acid in a protein - [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]

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**[http://zhanglab.ccmb.med.umich.edu/QUARK/ Quark server]

**[http://www.ks.uiuc.edu/Research/vmd/ VMD - Visual Molecular Dynamics]

*RNA modeling

**Secondary Structure

*** The [http://iimcb.genesilico.pl/comparna/methods/ methods page for CompaRNA] lists and provides links to several software and server-based programs for secondary structure prediction.

*** [http://web.cbio.uct.ac.za/~yves/nasp/ NASP] is a parallel program for identifying evolutionarily conserved nucleic acid secondary structures from nucleotide sequence alignments. See the companion [http://bioinformatics.oxfordjournals.org/content/27/17/2443.short?rss=1 article].

**3D Structure

*** [http://iimcb.genesilico.pl/modernaserver/ 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 [http://iimcb.genesilico.pl/moderna/ 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 [http://bioinformatics.oxfordjournals.org/content/27/17/2441.short?rss=1 article] for the server.

*RNA-protein modeling

**The [http://iimcb.genesilico.pl/index.php/software.html 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 [http://www.biomedcentral.com/1471-2105/12/348 article].

==References==

==Class Sandboxes==

{|

@@ Line 58: / Line 58: @@
 * nearly 75,000 X-ray crystallography, NMR, and cryo-EM structures
 * [http://www.pdb.org/pdb/statistics/contentGrowthChart.do?content=total&seqid=100 PDB statistics]
-* about 85% are crystallographic structures
+* about 85% are crystallographic structures - hydrogens anyone? [[Hydrogen in macromolecular models]]
 *[http://www.umass.edu/molvis/edm/cloud/index.htm 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
+** one gauge [[Resolution]] noted with a link on each PDB entry page
 ==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
+*[[Help:Getting Started in Proteopedia]]
 *User or Sandbox login
-*We encourage you all to become users of any sort. If you become a registered, you can save information in your userspace regardless of your overall contribution to public spaces.
+*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==
@@ Line 74: / Line 75: @@
 *PDB Entry Pages
 *User space Pages
-*Sandbox Pages
+*Sandbox Pages , see [[Help:Sandboxes]]
-*Workbench Pages
+*Workbench Pages ,see [[Proteopedia:Workbench]] and  [[Group:SMART:Workbench_SMART_Teams#]]
 *Interactive 3D Complements (I3DC) - [[Journal of Biological Inorganic Chemistry]]
 *Administrative
@@ Line 105: / Line 106: @@
 ***Biological Unit
 ***Missing pieces?; PDBsum link on Proteopedia entry pages helpful for this as well
-*Under adoptions on [http://molvis.sdsc.edu/fgij/index.htm main page] , there is [http://opm.phar.umich.edu/ Orientations of Proteins in Membranes (OPM) database] from the University of Michigan (Ann Arbor, Michigan, USA), which could be useful for several  proteins involved in endocrinology, example [[2rh1]]
+*Under adoptions on [http://molvis.sdsc.edu/fgij/index.htm main page] , there is [http://opm.phar.umich.edu/ 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
@@ Line 124: / Line 125: @@
 * [[Proteopedia:How to Make a Page]]
 *[[Help:Editing|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==
+==Proteopedia Scene Authoring and Adding Green Scene Links to a Page==
 *[[Scene authoring tools|Proteopedia's Scene Authoring Tools]]
+*To do:
 **Load a structure [[3ciy]] or previous scene
 **Set your scene. Undo/Redo features.
-**Save your scene
+*Save your scene
-**Add the scene to the page
+**Try it out and then add and improve. Repeat until you are happy with result.
-*Try it out and then add and improve. Repeat.
+*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.
@@ Line 160: / Line 167: @@
 *[[About Macromolecular Structure]]
 *[http://molvis.sdsc.edu/fgij/ FirstGlance in Jmol] is very useful for exploring PDB entries or upload structure files.
+*[http://biomodel.uah.es/en/scale/ 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.
 *[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"]
@@ Line 170: / Line 178: @@
 ===Small Molecule Visualization and Model Kits===
-*[http://chemagic.com/web_molecules/script_page_large.aspx CheMagic Virtual Molecular Model Kit]
+*[http://chemagic.com/draw.htm CheMagic Virtual Molecular Model Kit that works on most any device!!] - Uses JSmol
+*[http://biomodel.uah.es/en/DIY/JSME/ JSME Molecular Editor] - , the non-Java alternative to JME; uses JSmol <ref>B. Bienfait and P. Ertl, JSME: a free molecule editor in JavaScript, Journal of Cheminformatics 5:24 (2013) [http://www.jcheminf.com/content/5/1/24 article]</ref>
+*[http://chemagic.com/web_molecules/script_page_large.aspx CheMagic Virtual Molecular Model Kit] - Java based so only works on computers
 *[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://www.chemtube3d.com/index.html ChemTube3D] has interactive animations and structures of molecules and reactions important in chemistry.
 *[http://chemagic.com/web_molecules/acs.aspx Service allowing young people to look up a molecule and blow it up and put it back together]
+*[http://chemapps.stolaf.edu/jmol/docs/examples-12/ChemDoodleWeb/samples/sketcher_Jmol.html ChemDoodleWeb Integrated with Jmol]
+*[http://librairiedemolecules.education.fr/outils/scribmol/ Scribmol] is  a ChemDoodleWeb Integrated with Jmol application found at [http://librairiedemolecules.education.fr/outils/ a utilities page] (french) with other useful visualization tools.
+* [http://opentox.informatik.uni-freiburg.de/ches-mapper/ 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===
@@ Line 182: / Line 195: @@
 ===Authoring Scenes and Views in Proteopedia and beyond===
 *[[Proteopedia:Video Guide]]
+* [[Help:Getting Started in Proteopedia]]
 * [[Proteopedia:How to Make a Page]]
 *[[Help:Editing|How to edit pages in Proteopedia]] ? [[Ribosome|Example 1]], [[User:Wayne Decatur/Plant Viral Protein p19 Suppression of RNA Silencing|example 2]], and [[Avian Influenza Neuraminidase, Tamiflu and Relenza|example 3]] of edited topic pages.
@@ Line 199: / Line 213: @@
 *[[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.
 ===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]
+* Mutating an amino acid in a protein - [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]
@@ Line 215: / Line 228: @@
 **[http://zhanglab.ccmb.med.umich.edu/QUARK/ Quark server]
 **[http://www.ks.uiuc.edu/Research/vmd/ VMD - Visual Molecular Dynamics]
+*RNA modeling
+**Secondary Structure
+*** The [http://iimcb.genesilico.pl/comparna/methods/ methods page for CompaRNA] lists and provides links to several software and server-based programs for secondary structure prediction.
+*** [http://web.cbio.uct.ac.za/~yves/nasp/ NASP] is a parallel program for identifying evolutionarily conserved nucleic acid secondary structures from nucleotide sequence alignments.  See the companion [http://bioinformatics.oxfordjournals.org/content/27/17/2443.short?rss=1 article].
+**3D Structure
+*** [http://iimcb.genesilico.pl/modernaserver/ 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 [http://iimcb.genesilico.pl/moderna/ 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 [http://bioinformatics.oxfordjournals.org/content/27/17/2441.short?rss=1 article] for the server.
+*RNA-protein modeling
+**The [http://iimcb.genesilico.pl/index.php/software.html 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 [http://www.biomedcentral.com/1471-2105/12/348 article].
+==References==
+<references/>
 ==Class Sandboxes==
 {|