Worldwide Protein Data Bank: Difference between revisions
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*Protein Data Bank Japan, [http://www.pdbj.org PDBj] |
*Protein Data Bank Japan, [http://www.pdbj.org PDBj] |
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*Biological Magnetic Resonance Data Bank, [http://www.bmrb.wisc.edu/ BMRB] (USA) |
*Biological Magnetic Resonance Data Bank, [http://www.bmrb.wisc.edu/ BMRB] (USA) |
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The wwPDB was founded in 2003 by [http://www.rcsb.org/pdb RCSB PDB (USA)], [http://www. |
The wwPDB was founded in 2003 by [http://www.rcsb.org/pdb RCSB PDB (USA)], [http://www.pdbe.org/ PDBe (Europe)] and [http://www.pdbj.org PDBj (Japan)]. In 2006 [http://www.bmrb.wisc.edu/ BMRB (USA)] joined the wwPDB. |
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Each member's site can accept structural data and process the data. The processed data is sent to the "archive keeper", which is agreed to be RCSB PDB. Only the archive keeper can modify the database; this ensures that there is only one version of the data. The modified database is then made available to the other wwPDB members, each of whom makes the resulting structure files available through their websites to the public. (Data is accessed from the wwPDB website itself only through links to the member websites.) The member sites are more than just mirrors of the archive keeper, because the members offer different tools on their websites for processing the structures in the database. |
Each member's site can accept structural data and process the data. The processed data is sent to the "archive keeper", which is agreed to be RCSB PDB. Only the archive keeper can modify the database; this ensures that there is only one version of the data. The modified database is then made available to the other wwPDB members, each of whom makes the resulting structure files available through their websites to the public. (Data is accessed from the wwPDB website itself only through links to the member websites.) The member sites are more than just mirrors of the archive keeper, because the members offer different tools on their websites for processing the structures in the database. |
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:The four member organizations: |
:The four member organizations: |
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:[http://www.rcsb.org/pdb RCSB PDB], Research Collaboratory for Structural Bioinformatics Protein Databank (USA) |
:[http://www.rcsb.org/pdb RCSB PDB], Research Collaboratory for Structural Bioinformatics Protein Databank (USA) |
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:[http://www.pdbe.org PDBe], Protein Data Bank in Europe |
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:[http://www.ebi.ac.uk/msd MSD-EBI], European Bioinformatics Institute, Macromolecular Structure Database Group |
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:[http://www.pdbj.org PDBj], Protein Data Bank Japan |
:[http://www.pdbj.org PDBj], Protein Data Bank Japan |
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:[http://www.bmrb.wisc.edu/ BMRB], Biological Magnetic Resonance Data Bank (USA) |
:[http://www.bmrb.wisc.edu/ BMRB], Biological Magnetic Resonance Data Bank (USA) |
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Revision as of 15:45, 1 July 2010
The Worldwide Protein Data Bank, wwPDB, is an organization whose mission, according to its website,[1] is "to maintain a single Protein Data Bank Archive of macromolecular structural data that is freely and publicly available to the global community." Given the open access goal, it is somewhat ironic that the announcement of the collaborative was made in a pay-for-access journal (Nature Structual Biology).[2]
The organization has four members:[3]
- Research Collaboratory for Structural Bioinformatics Protein Database, RCSB PDB (USA)
- Protein Data Bank in Europe, PDBe
- Protein Data Bank Japan, PDBj
- Biological Magnetic Resonance Data Bank, BMRB (USA)
The wwPDB was founded in 2003 by RCSB PDB (USA), PDBe (Europe) and PDBj (Japan). In 2006 BMRB (USA) joined the wwPDB.
Each member's site can accept structural data and process the data. The processed data is sent to the "archive keeper", which is agreed to be RCSB PDB. Only the archive keeper can modify the database; this ensures that there is only one version of the data. The modified database is then made available to the other wwPDB members, each of whom makes the resulting structure files available through their websites to the public. (Data is accessed from the wwPDB website itself only through links to the member websites.) The member sites are more than just mirrors of the archive keeper, because the members offer different tools on their websites for processing the structures in the database.
Accomplishments (taken from wwPDB annual reports)
- 2008 The wwPDB now requires that, in addition to atomic coordinates, structure factor amplitudes and intensities (for crystal structure depositions) and NMR restraints (for NMR structure depositions) must be deposited as a prerequisite for receiving a PDB ID.
- 2007 Rolled out a remediated PDB. Remediation included changing the nomenclature to conform to IUPAC standards.[4]
References
- ^ Worldwide Protein Data Bank. URL: http://www.wwpdb.org. Accessed on: April 22, 2009.
- ^ Berman H, Henrick K, Nakamura H (2003). "Announcing the worldwide Protein Data Bank". Nat. Struct. Biol. 10 (12): 980. doi:10.1038/nsb1203-980. PMID 14634627.
{{cite journal}}: Unknown parameter|month=ignored (help)CS1 maint: multiple names: authors list (link) - ^ H., Berman (2007). "The worldwide Protein Data Bank (wwPDB): ensuring a single, uniform archive of PDB data" (PDF). Nucleic Acids Res. 35 (Database issue): D301–D303. doi:10.1093/nar/gkl971. PMC 1669775. PMID 17142228. Retrieved 1/3/2008.
{{cite journal}}: Check date values in:|accessdate=(help); Unknown parameter|coauthors=ignored (|author=suggested) (help); Unknown parameter|month=ignored (help) - ^ H., Berman (2008). "Remediation of the protein data bank archive". Nucleic Acids Res. 36 (Database issue): D426–D433. doi:10.1093/nar/gkm937. PMC 2238854. PMID 18073189. Retrieved 1/3/2008.
{{cite journal}}: Check date values in:|accessdate=(help); Unknown parameter|coauthors=ignored (|author=suggested) (help); Unknown parameter|month=ignored (help)
See also
External links
The parent organization: wwPDF