PROTEIN DATA BANK....(PDB)

The Protein Data Bank (PDB) is a repository for the 3-D structural data of large biological molecules, such as proteins and nucleic acids. (See also crystallographic database). The data, typically obtained by X-ray crystallography or NMR spectroscopy and submitted by biologists and biochemists from around the world, are freely accessible on the internet. The PDB is overseen by an organization called the Worldwide Protein Data Bank, wwPDB.
The PDB is a key resource in areas of structural biology, such as structural genomics. Most major scientific journals, and some funding agencies, such as the NIH in the USA, now require scientists to submit their structure data to the PDB. If the contents of the PDB are thought of as primary data, then there are hundreds of derived (i.e., secondary) databases that categorize the data differently. For example, both SCOP and CATH categorize structures according to type of structure and assumed evolutionary relations; GO categorize structures based on genes.<sup>[1]

 HISTORY...</sup>
The PDB originated as a grassroots effort.^[1] In 1971, Walter Hamilton of the Brookhaven National Laboratory agreed to set up the data bank at Brookhaven. Upon Hamilton's death in 1973, Tom Koeztle took over direction of the PDB. In January 1994, Joel Sussman was appointed head of the PDB. In October 1998,^[2] the PDB was transferred to the Research Collaboratory for Structural Bioinformatics (RCSB); the transfer was completed in June 1999. The new director was Helen M. Berman of Rutgers University (one of the member institutions of the RCSB).^[3] In 2003, with the formation of the wwPDB, the PDB became an international organization. Each of the four members of wwPDB can act as deposition, data processing and distribution centers for PDB data. The data processing refers to the fact that wwPDB staff review and annotates each submitted entry. The data are then automatically checked for plausibility. (The source code for this validation software has been made available to the public at no charge.

 

Crystal structure of a LexA protein from Thermotoga maritima

The PDB database is updated weekly (on Tuesday). Likewise, the PDB Holdings List is also updated weekly. As of 21 September 2010 (2010 -09-21)^[update], the breakdown of current holdings was as follows:

Experimental Method	Proteins	Nucleic Acids	Protein/Nucleic Acid complexes	Other	Total
X-ray diffraction	55480	1231	2605	17	59333
NMR	7512	925	162	7	8606
Electron microscopy	214	17	77	0	308
Hybrid	24	1	1	1	27
Other	126	4	4	13	147
Total:	63356	2178	2849	38	68421

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