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Nucleic Acids Research Advance Access published online on December 11, 2007
Nucleic Acids Research, doi:10.1093/nar/gkm937
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© 2007 The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

Database Issue

Remediation of the protein data bank archive

Kim Henrick1, Zukang Feng2, Wolfgang F. Bluhm3, Dimitris Dimitropoulos1, Jurgen F. Doreleijers4, Shuchismita Dutta2, Judith L. Flippen-Anderson2, John Ionides1, Chisa Kamada5, Eugene Krissinel1, Catherine L. Lawson2, John L. Markley4, Haruki Nakamura5, Richard Newman1, Yukiko Shimizu5, Jawahar Swaminathan1, Sameer Velankar1, Jeramia Ory2, Eldon L. Ulrich4, Wim Vranken1, John Westbrook2, Reiko Yamashita5, Huanwang Yang2, Jasmine Young2, Muhammed Yousufuddin2 and Helen M. Berman2,*

1MSD-EBI, EMBL Outstation-Hinxton, Cambridge CB10 1SD, UK, 2RCSB Protein Data Bank, Department of Chemistry and Chemical Biology, Rutgers, The State University of New Jersey, 610 Taylor Road, Piscataway, NJ 08854-8087, USA, 3RCSB Protein Data Bank, San Diego Supercomputer Center and the Skaggs School of Pharmacy and Pharmaceutical Sciences at the University of California, San Diego, 9500 Gilman Drive, Mailcode 0743, La Jolla, CA 92093, USA, 4BioMagResBank, University of Wisconsin-Madison, Department of Biochemistry, 433 Babcock Drive, Madison, WI 53706, USA and 5PDBj, Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Osaka 565-0871, Japan

*To whom correspondence should be addressed. Tel: +1 732 445 4667; Fax: +1 732 445 4320; Email: berman{at}rcsb.rutgers.edu

Received September 13, 2007. Revised October 8, 2007. Accepted October 11, 2007.

The Worldwide Protein Data Bank (wwPDB; wwpdb.org) is the international collaboration that manages the deposition, processing and distribution of the PDB archive. The online PDB archive at ftp://ftp.wwpdb.org is the repository for the coordinates and related information for more than 47 000 structures, including proteins, nucleic acids and large macromolecular complexes that have been determined using X-ray crystallography, NMR and electron microscopy techniques. The members of the wwPDB–RCSB PDB (USA), MSD-EBI (Europe), PDBj (Japan) and BMRB (USA)–have remediated this archive to address inconsistencies that have been introduced over the years. The scope and methods used in this project are presented.


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