User:Wayne Decatur/NASCE2011: Difference between revisions
From Proteopedia
Jump to navigationJump to search
mNo edit summary |
|||
| Line 7: | Line 7: | ||
==Introduction to Proteopedia== | ==Introduction to Proteopedia== | ||
* Main Page | * Main Page | ||
* | * Sightseeing by way of example <nowiki>"</nowiki>Case Studies<nowiki>"</nowiki> / "<nowiki>"</nowiki>User Narratives<nowiki>"</nowiki> | ||
**Topics | **Topics | ||
***main page--->[[Ribosome]] structure, spin, toggles, list, contributors --->[[Ribosome#The Peptidyl Transferase Is A Ribozyme||page particular section]] ---> [[Large Ribosomal Subunit of Haloarcula#The ribosome is a ribozyme - protein DOES NOT participate directly in the chemistry of peptide bond synthesis:|another page]] green links | ***main page--->[[Ribosome]] structure, spin, toggles, list, contributors --->[[Ribosome#The Peptidyl Transferase Is A Ribozyme||page particular section]] ---> [[Large Ribosomal Subunit of Haloarcula#The ribosome is a ribozyme - protein DOES NOT participate directly in the chemistry of peptide bond synthesis:|another page]] green links | ||
| Line 45: | Line 45: | ||
*Advanced Options | *Advanced Options | ||
**Console | **Console | ||
**[http://chemapps.stolaf.edu/jmol/docs/examples-11/new.htm?topic=103 ''Compare'' Command Demonstration] | **[http://chemapps.stolaf.edu/jmol/docs/examples-11/new.htm?topic=103 ''Compare'' Command Demonstration] | ||
* | **Sculpting - Simple example of that [http://chemagic.com/web_molecules/acs.aspx here] | ||
**3D options - Demo with [[Hormone]] | |||
==The Structure Data== | ==The Structure Data== | ||
* Centers around an [[Atomic coordinate file]] | * Centers around an [[Atomic coordinate file]] | ||
*Experimental vs theoretical sources | * Experimental vs theoretical sources | ||
==Protein Data Bank== | ==Protein Data Bank== | ||
| Line 59: | Line 57: | ||
* about 85% are crystallographic structures | * about 85% are crystallographic structures | ||
*[http://www.umass.edu/molvis/edm/cloud/index.htm Metaphor with electron density] | *[http://www.umass.edu/molvis/edm/cloud/index.htm Metaphor with electron density] | ||
*Caveat: [http://www.umass.edu/molvis/edm/cloud/edm2.htm Keep in mind these are models] - Not all | *Caveat: [http://www.umass.edu/molvis/edm/cloud/edm2.htm Keep in mind these are models] - Not all models created equally | ||
==Proteopedia== | ==Proteopedia== | ||
| Line 109: | Line 107: | ||
***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 | ||
==Structural Biology for Non-structural Biologists== | ==Structural Biology for Non-structural Biologists== | ||
| Line 147: | Line 142: | ||
***[http://chemcanvas.sourceforge.net/chemWin.html Works with small molecules too] and even can do energy minimization with them | ***[http://chemcanvas.sourceforge.net/chemWin.html Works with small molecules too] and even can do energy minimization with them | ||
***[http://www.chemtube3d.com/Diels-Alder%20-%20Stereochemistry%20of%20the%20diene%20%28cis-trans%29.html Can be used to show chemical reactions] | ***[http://www.chemtube3d.com/Diels-Alder%20-%20Stereochemistry%20of%20the%20diene%20%28cis-trans%29.html Can be used to show chemical reactions] | ||
*Not all models OR EVEN PORTIONS of models created equally - Caveat: [http://www.umass.edu/molvis/edm/cloud/edm2.htm Keep in mind these are models] - | |||
*Assessing structure | |||
**[[Resolution]] noted with a link on each PDB entry page | |||
**[[Temperature factors]], also see demonstration [http://www.umass.edu/molvis/edm/cloud/edm2.htm here] | |||
**Gaps, i.e. missing pieces (see above) | |||
==Resources== | ==Resources== | ||
