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Nucleic Acids Research 2005 33(Database Issue):D233-D237; doi:10.1093/nar/gki057
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Nucleic Acids Research, 2005, Vol. 33, Database issue D233-D237
© 2005, the authors
Nucleic Acids Research, Vol. 33, Database issue © Oxford University Press 2005; all rights reserved

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

Nita Deshpande1, Kenneth J. Addess1, Wolfgang F. Bluhm1, Jeffrey C. Merino-Ott1, Wayne Townsend-Merino1, Qing Zhang1, Charlie Knezevich1, Lie Xie1, Li Chen3, Zukang Feng3, Rachel Kramer Green3, Judith L. Flippen-Anderson3, John Westbrook3, Helen M. Berman3 and Philip E. Bourne1,2,*

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

* To whom correspondence should be addressed. Tel: +1 858 534 8301; Fax: +1 858 822 0873; Email: bourne{at}sdsc.edu

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

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.

The online version of this article has been published under an open access model. Users are entitled to use, reproduce, disseminate, or display the open access version of this article for non-commercial purposes provided that: the original authorship is properly and fully attributed; the Journal and Oxford University Press are attributed as the original place of publication with the correct citation details given; if an article is subsequently reproduced or disseminated not in its entirety but only in part or as a derivative work this must be clearly indicated. For commercial re-use permissions, please contact journals.permissions{at}oupjournals.org.


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