Brookhaven Protein Data Base

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Brookhaven Protein Data Base

The BPDB archive’s experimental findings describing to (the point of) atomic resolution, the 3D structures of > 3000 proteins, nucleic acids and other biological macromolecules.

With advances in storage and hardware speed, older standards are often retired. The name changed to Protein Data Bank and resides in Cambridge instead of Long Island, New York.
References in periodicals archive ?
In the Protein Data Bank, we found structures of three different drugs bound to GCase.
Kinemage scripts may be generated or "authored" with any text editor if the author follows the proper formatting but, for generating molecular kinemages from coordinate files such as Protein Data Bank files, there is a menu-driven authoring program called Prekin.
Another development involves the easily accessible and rapidly expanding databases of molecular structures, such as Brookhaven National Laboratory's protein data bank, where researchers can build upon other researchers' modeling efforts.
And a protein data bank containing 700,000 amino acids can be searched in less than 10 minutes.
Further, integrating data from FORMA s X-ray crystallography efforts across product pipeline targets with CS-Map technology interrogation of the surfaces for all human proteins in the Protein Data Bank (PDB) (~16,000) enabled the design and synthesis of shape-directed compound libraries biased toward shapes of druggable pockets on protein surfaces.
The Basic Local Alignment Search Tool (BLAST) (55), and RCSB Protein Data Bank (56) were used to achieve this goal.
If the protein has a link to the Protein Data Bank (PDB), clicking one of the entries will open a new window at the PDB site (Table 1).
Other links lead to the Department of Energy's site on pharmacogenomics, the Pharmaceutical Research and Manufacturers of America's genomics resource guide, the Human Genetic Cell Repository, dbSNP (a database of single-nucleotide polymorphisms), the Protein Data Bank, and PharmGKB.
NIST has completed the production of the latest Protein Data Bank (PDB) CD-ROM set.
As co-director of the crystallography group of the Northeast Structural Genomics, Hunt has co-authored almost 500 depositions into the Protein Data Bank and focused a major effort on understanding the physiochemical properties controlling protein crystallization.
The availability of about 77,000 protein structures in Protein Data Bank (PDB) (8) and a great deal of experimental works on the thermodynamic stability of proteins have provided a wealth of information which can be used for the development of empirical functions that relate thermodynamic and structural parameters.
To handle the deluge of protein data, NIST, in partnership with Rutgers University and the UCSD, formed the RCSB, which acquired the Protein Data Bank in 1997.