Protein Data Bank: Difference between revisions

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Proteopedia Page Contributors and Editors (what is this?)Proteopedia Page Contributors and Editors (what is this?)

Eric Martz, Joel L. Sussman, Jaime Prilusky, Wayne Decatur

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-The [http://www.wwpdb.org World Wide Protein Data Bank] (wwPDB)<ref>PMID: 14634627</ref><ref>PMID: 17142228</ref> is the internationally recognized sole repository of all published, empirically-determined atomic resolution macromolecular three-dimensional (3D) structure data. Founded in 1971 by Drs. Edgar Meyer and Walter Hamilton at [http://www.bnl.gov Brookhaven National Laboratory], management of the Protein Data Bank was headed by Tom Koestle until 1994 and then by [http://www.weizmann.ac.il/~joel Joel L. Sussman] till 1999, when it was transferred to members of the [http://home.rcsb.org/ Research Collaboratory for Structural Bioinformatics (RCSB)]. Rutgers University is the lead site and is currently under the direction of [http://en.wikipedia.org/wiki/Helen_M._Berman Helen M. Berman]. In 2008, it has three official branches: the Research Collaboratory for Structural Bioinformatics (USA), the European Bioinformatics Institute (UK), and the Protein Data Bank Japan.
+The [http://www.wwpdb.org World Wide Protein Data Bank] (wwPDB)<ref>PMID: 14634627</ref><ref>PMID: 17142228</ref> is the internationally recognized sole repository<ref>PMID: 30357364</ref> of all published, empirically-determined atomic resolution macromolecular three-dimensional (3D) structure data. Founded in 1971 by Drs. Edgar Meyer and Walter Hamilton at [http://www.bnl.gov Brookhaven National Laboratory]<REF>PMID:875032</REF><REF>PMID:10089483</REF>, management of the Protein Data Bank was headed by Tom Koestle until 1994 and then by [http://www.weizmann.ac.il/~joel Joel L. Sussman] till 1999, when it was transferred to members of the [http://home.rcsb.org/ Research Collaboratory for Structural Bioinformatics (RCSB)]. RCSB is managed at Rutgers University and the San Diego Supercomputer Center. It was directed by [http://en.wikipedia.org/wiki/Helen_M._Berman Helen M. Berman] until July 2014, when Stephen K. Burley took over the directorship<ref>[http://www.rcsb.org/pdb/general_information/news_publications/newsletters/2014q4/home.html#one2 Leadership Transition], RCSB Newsletter, Fall 2014.</ref>. In 2008, the PDB has three official branches: the Research Collaboratory for Structural Bioinformatics (RCSB, USA), the European Bioinformatics Institute (PDBe, UK), and the Protein Data Bank Japan (PDBj, Osaka).
 ==New Releases Cycle==
-The wwPDB releases new entries once per week. These can be seen by clicking on the most recent release date, shown at the upper right of the main page at [http://pdb.org PDB.Org]. In 2007, 7,280 new entries were released (an average of 140/week).
+The wwPDB releases new entries once per week. These can be seen by clicking on the most recent release date, shown at the upper right of the main page at [http://pdb.org PDB.Org]. In 2007, 7,280 new entries were released (an average of 140/week). In 2011, 8,101 new entries were released (average 155/week).<ref>In May 2012, the following numbers were reported by advanced search on release dates at RCSB. 2011: 8,101. 2010: 7907. 2009: 7388. 2008: 6964. 2007: 7199.</ref>
 While the traditional entry consisted of an [[Atomic coordinate file | atomic coordinate file]] molecular model, more recently, the '''experimental data''' (structure factors in the case of crystallography) have been deposited along with the the model. After February 1, 2008, deposition of experimental data is required along with all new entries.
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 ===See Also in Proteopedia===
+*[[AlphaFold#AlphaFold_Database_of_Predictions|Database of structures predicted by AlphaFold2]].
+*[[ModelArchive]] for [[Empirical models|non-empirical]] models.
 *[[About Macromolecular Structure]], a list of pages in Proteopedia
 *[[Atomic coordinate file]]
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 *[http://www.pdb.org RCSB PDB]
 *[http://en.wikipedia.org/wiki/Protein_data_bank Protein Data Bank in Wikipedia]
-*[http://pdbwiki.org/index.php/Protein_Data_Bank Protein Data Bank at PDBWiki.Org]
+*"Synergies between the Protein Data Bank and the community", 2021<ref name="synergies">PMID: 33963295</ref>.
 *Berman H, Henrick K, Nakamura H, Markley JL. The worldwide Protein Data Bank (wwPDB): ensuring a single, uniform archive of PDB data.  Nucleic Acids Res.35:D301-3. (2007) PMID:[http://www.ncbi.nlm.nih.gov/pubmed/17142228 17142228].
 *Berman HM <i>et al.</i>, The Protein Data Bank, Acta Crystallogr D Biol Crystallogr.58:899-907 (2002). PMID:[http://www.ncbi.nlm.nih.gov/pubmed/12037327 12037327]
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 *Sussman JL, Lin D, Jiang J, Manning NO, Prilusky J, Ritter O, Abola EE (1998). "Protein data bank (PDB): a database of 3D structural information of biological macromolecules". ''Acta Cryst'' '''D54''':1078-1084. PMID 10089483.
 *[http://www.umass.edu/microbio/rasmol/1st_xtls.htm Earliest Solutions for Macromolecular Crystal Structures]
+*[https://www.rcsb.org/news/feature/66acd3c8eb1f4889a9e4432b 'PDB Archive Serves Structures Determined by Integrative and Hybrid Methods (IHM) (August 2024)']
 *See also [[Proteopedia:Policy#Theoretical_Models | Theoretical Models]].
-==Literature Cited==
+==References and Notes==
 <references />