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Briefings in Bioinformatics 2004 5(1):23-30; doi:10.1093/bib/5.1.23
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© Henry Stewart Publications

Special Issue papers

The Protein Data Bank and lessons in data management

Philip E. Bourne
Professor of Pharmacology at UCSD, Director of Integrative Biosciences at SDSC, and a Co-Director of the PDB. His research interests focus on structural bioinformatics and high performance computing as applied to problems in genomics and proteomics.

John Westbrook
Research Associate Professor of Chemistry and Chemical Biology at Rutgers and a Co-Director of the PDB. His research interests include bioinformatics, computational biology and ontology management.

Helen M. Berman
Board of Governors Professor of Chemistry and Chemical Biology at Rutgers, and Director of the PDB. Her research interests include structural biology and bioinformatics, with a special focus on protein—nucleic acid interactions


Phillip E. Bourne, Research Collaboratory for Structural Bioinformatics, Department of Pharmacology and San Diego Supercomputer Center, University of California San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0537, USA Tel: +1 858 534 8301 Fax: +1 858 822 0873 E-mail: bourne{at}sdsc.edu

The Protein Data Bank (PDB) is a widely used biological database of macromolecular structures with a long history. This history is treated as lessons learned and is used to highlight what are believed to be the best practices important to developers of biological databases today. While the focus is on data quality, data representation and the information technology to support these data, the non-data and technology issues cannot be ignored. The role of the human factor in the form of users, collaborators, scientific society and ad hoc committees is also included.

Keywords: PDB, mmCIF, macromolecular structure data, the human factor, data uniformity


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