User:Wayne Decatur/NASCE2011: Difference between revisions
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*** learn of a structure in a meeting (Robert Milllar talk on Saturday) ---> [http://www.ncbi.nlm.nih.gov/pubmed/17962520 Pubmed search result]---> [[2rh1]] | *** learn of a structure in a meeting (Robert Milllar talk on Saturday) ---> [http://www.ncbi.nlm.nih.gov/pubmed/17962520 Pubmed search result]---> [[2rh1]] | ||
****Sites | ****Sites | ||
**** | ****ConSurf | ||
****Firstglance in Jmol | ****Firstglance in Jmol | ||
***[http://www.nature.com/nature/journal/v475/n7354/full/nature10236.html new publication] ---> [[3rze]] Sites | ***[http://www.nature.com/nature/journal/v475/n7354/full/nature10236.html new publication] ---> [[3rze]] Sites | ||
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*[[Main Page|Proteopedia]] - interactive 3D encylopedia of macromolecular structures and structural biology resources to which scientists contribute and use to share structural biology content | *[[Main Page|Proteopedia]] - interactive 3D encylopedia of macromolecular structures and structural biology resources to which scientists contribute and use to share structural biology content | ||
*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. | |||
==Types of Proteopedia pages== | ==Types of Proteopedia pages== | ||
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** Example [[1p3v]] (PDB 4 digit alphanumeric accession number) | ** Example [[1p3v]] (PDB 4 digit alphanumeric accession number) | ||
***Conservation: , explanation, and see also [http://consurfdb.tau.ac.il/comparison.php The ConSurf Database] and [http://consurf.tau.ac.il/ The ConSurf Server] Other examples: [[4enl]] or [[5cyt]] | ***Conservation: , explanation, and see also [http://consurfdb.tau.ac.il/comparison.php The ConSurf Database] and [http://consurf.tau.ac.il/ The ConSurf Server] Other examples: [[4enl]] or [[5cyt]] | ||
***Show how to use | ***Show how to use ConSurf | ||
==FirstGlance in Jmol== | ==FirstGlance in Jmol== | ||
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***Biological Unit | ***Biological Unit | ||
***Missing pieces?; PDBsum link on Proteopedia entry pages helpful for this as well | ***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]] | |||
==Structural Biology for Non-structural Biologists== | ==Structural Biology for Non-structural Biologists== | ||
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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. | ||
**Example - [http://polyview.cchmc.org/cgi-bin/get_image_3d.cgi?IMG=12963556621229&JOB=395c698c611181d 3pla] | **Example - [http://polyview.cchmc.org/cgi-bin/get_image_3d.cgi?IMG=12963556621229&JOB=395c698c611181d 3pla] | ||
**Makes animations too and/or morphs | **Makes animations too and/or morphs as well using multiple model structures | ||
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**[[Temperature factors]], also see demonstration [http://www.umass.edu/molvis/edm/cloud/edm2.htm here] | **[[Temperature factors]], also see demonstration [http://www.umass.edu/molvis/edm/cloud/edm2.htm here] | ||
**Gaps, i.e. missing pieces (see above) | **Gaps, i.e. missing pieces (see above) | ||
==Resources== | ==Resources== | ||