The RCSB Protein Data Bank: a redesigned query system and relational database based on the mmCIF schema

Deshpande, Nita
Addess, Kenneth J.
Bluhm, Wolfgang F.
Merino-Ott, Jeffrey C.
Townsend-Merino, Wayne
Zhang, Qing
Knezevich, Charlie
Xie, Lie
Chen, Li
Feng, Zukang
Kramer Green, Rachel
Flippen-Anderson, Judith L.
Westbrook, John
Berman, Helen M.
Bourne, Philip E.

¹San Diego Supercomputer Center, University of California San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA
²Department of Pharmacology, University of California San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA
³Department of Chemistry and Chemical Biology, Rutgers, The State University of New Jersey, 610 Taylor Road, Piscataway, NJ 08854-8087, USA

Received September 15, 2004; Revised and Accepted October 1, 2004

^*To whom correspondence should be addressed. Tel: +1 858 534 8301; Fax: +1 858 822 0873; Email: [email protected]

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Nucleic Acids Research 33:p D233-D237, January 1, 2005.

The Protein Data Bank (PDB) is the central worldwide repository for three-dimensional (3D) structure data of biological macromolecules. The Research Collaboratory for Structural Bioinformatics (RCSB) has completely redesigned its resource for the distribution and query of 3D structure data. The re-engineered site is currently in public beta test at http://pdbbeta.rcsb.org. The new site expands the functionality of the existing site by providing structure data in greater detail and uniformity, improved query and enhanced analysis tools. A new key feature is the integration and searchability of data from over 20 other sources covering genomic, proteomic and disease relationships. The current capabilities of the re-engineered site, which will become the RCSB production site at http://www.pdb.org in late 2005, are described.