Protein Data Bank: Difference between revisions

Revision as of 05:29, 15 June 2008

The World Wide Protein Data Bank (wwPDB) is the internationally recognized sole repository of all published, empirically-determined macromolecular three-dimensional (3D) structure data. 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.

New Releases CycleNew 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 [1]. In 2007, 7,280 new entries were released (an average of 140/week).

While the traditional entry consisted of an 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.

Many derivative databases copy, derive information from, or add value to the atomic coordinate files available from the wwPDB. Often, these automatically update their databases weekly, shortly after the new releases become available at the PDB. Proteopedia is one example.

PDB StatisticsPDB Statistics

At [2], at the upper right corner of the main page, click on PDB Statistics for a wealth of interesting information, including proteins solved by multiple experimental methods, sequence redundancy in the PDB, the distribution of resolutions, the 100 journals that have published the most new macromolecular structures, and graphs of the growth of the database (under Content Growth).

More About The Protein Data BankMore About The Protein Data Bank

World Wide Protein Data Bank
RCSB PDB
Protein Data Bank in Wikipedia
Protein Data Bank at PDBWiki.Org
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:17142228.
Berman HM et al., The Protein Data Bank, Acta Crystallogr D Biol Crystallogr.58:899-907 (2002). PMID:12037327
H.M. Berman, J. Westbrook, Z. Feng, G. Gilliland, T.N. Bhat, H. Weissig, I.N. Shindyalov, P.E. Bourne: The Protein Data Bank. Nucleic Acids Research, 28 pp. 235-242 (2000). PMID:10592235.
Earliest Solutions for Macromolecular Crystal Structures

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 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]. In 2007, 7,280 new entries were released (an average of 140/week).
-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.
+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.
 Many derivative databases '''copy, derive information from, or add value to''' the [[Atomic coordinate file | atomic coordinate files]] available from the wwPDB. Often, these automatically update their databases weekly, shortly after the new releases become available at the PDB. Proteopedia is one example.