User:Wayne Decatur/NASCE2011: Difference between revisions
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*[[Help:Getting Started in Proteopedia]] | *[[Help:Getting Started in Proteopedia]] | ||
*User or Sandbox login | *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== | ==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 ,see [[Proteopedia:Workbench]] and [[Group:SMART:Workbench_SMART_Teams#]] | ||
*Interactive 3D Complements (I3DC) - [[Journal of Biological Inorganic Chemistry]] | *Interactive 3D Complements (I3DC) - [[Journal of Biological Inorganic Chemistry]] | ||
*Administrative | *Administrative | ||
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*[[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://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://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"] | ||
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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/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://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] | ||
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*RNA-protein modeling | *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]. | **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== | ==Class Sandboxes== | ||
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