User:Wayne Decatur/Biochem642 Molecular Visualization 2010 Fall Sessions: Difference between revisions

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==Introduction==
==Introduction==
*[http://nobelprize.org/nobel_prizes/chemistry/laureates/2009/ Nobel prizes 2009] studies of the structure and function of [[Ribosome|the ribosome structure]].
*Logistical information about class today and next week and problem sets
*Importance of Structural Biology
**Important for understanding function
**helpful representations and models for people learning
**[http://nobelprize.org/nobel_prizes/chemistry/laureates/2009/ Nobel prizes 2009] studies of the structure and function of [[Ribosome|the ribosome structure]].
*Structural Biology for Non-structural Biologists
**[http://www.umass.edu/microbio/chime/top5.htm MolviZ "Top 5"]
**items III-V pertinent today
**particularly item III shows us how we can explore structures.
*Proteopedia - interactive 3D encylopedia of macromolecular structures and structural biology resources to which scientists contribute and use to share structural biology content
**Proteopedia allows sharing of structural biology data in a 3D, interactive manner
***[[Plant Viral Protein p19 Suppression of RNA Silencing]]
***[[Glutamate receptor]]
**Resources and information
***[[About Macromolecular Structure]]
***[[Help:Searching|Searching]]
****2 means - example search net charge
 
**Proteopedia has an entry for every PDB entry with links to useful items
***PDB 4 digit alphanumeric accession number, similar to a PubMed ID or Genbank sequence accession number
***Conservation: [[5cyt]], explanation, and see also [http://consurfdb.tau.ac.il/comparison.php The ConSurf Database] and [http://consurf.tau.ac.il/ The ConSurf Server] (Note: This is also item IV at [http://www.umass.edu/microbio/chime/top5.htm MolviZ "Top 5"].)
***RCSB = Protein Data Bank - use link under [[5cyt]] to RCSB
 
*Protein Data Bank
** X-ray crystallography, NMR, and cryo-EM structures - total 68,840
**From FAQ: "Since October 15, 2006, PDB depositions have been restricted to atomic coordinates that are substantially determined by experimental measurements on specimens containing biological macromolecules."
**Slide on overview of crystallography, NMR, and cryo-EM structures
**I'll point you to [http://www.umass.edu/molvis/workshop/barcel10.htm Eric Martz's recent workshop] if you seek more information in 3D-interactive examples on on resolution, temperature (b-factors, and electron density maps.
 
 
***[[Plant Viral Protein p19 Suppression of RNA Silencing]]
 
*Structures:  
*Structures:  
**X-ray crystallography and [[Resolution|resolution]]
**X-ray crystallography and [[Resolution|resolution]]
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