International
Tables for
Crystallography
Volume G
Definition and exchange of crystallographic data
Edited by S. R. Hall and B. McMahon

International Tables for Crystallography (2006). Vol. G, ch. 5.5, p. 539

Section 5.5.1. Introduction

J. D. Westbrook,a* H. Yang,a Z. Fenga and H. M. Bermana

aProtein Data Bank, Research Collaboratory for Structural Bioinformatics, Rutgers, The State University of New Jersey, Department of Chemistry and Chemical Biology, 610 Taylor Road, Piscataway, NJ 08854-8087, USA
Correspondence e-mail:  jwest@rcsb.rutgers.edu

5.5.1. Introduction

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The Protein Data Bank (PDB) is an archive for macromolecular structures (Bernstein et al., 1977[link]; Berman et al., 2000[link]) and a major component of a global resource for macromolecular structural science (Berman et al., 2003[link]). The scale of its data handling operations is large, and depends on the effective exploitation of the latest developments in the science and technology of informatics. A significant component of its data storage and retrieval strategy is the management of structural data in mmCIF format with appropriate extensions.

Over its 30-year history, the PDB archive has grown from seven entries in 1973 to a collection of over 30 000 structures as of May 2005. The growth in the size of the archive has been accompanied by increases in both data content and in the structural complexity of individual entries. As the PDB has grown, there has been a significant broadening of its user community. In response to this change, the role of the PDB has expanded from being simply a provider of structure data files to providing a key information resource for the structural biology community.

Looking forward, an acceleration in the growth of the PDB archive is anticipated owing to developments in high-throughput structural determination methodologies and worldwide structural genomics efforts. To support the continued growth and evolution of the PDB archive, a framework is required that supports automation and scalability, and that can adapt to changes in both data content and delivery technology.

At the core of the PDB informatics infrastructure is an ontology of data definitions which electronically encode domain information in the form of precise definitions, examples and controlled vocabularies. In addition to domain information, data definitions also encode information such as data type, data relationships, range restrictions and presentation units.

The software-accessible PDB exchange data dictionary (Appendix 3.6.2[link] ) is the key part of the PDB informatics infrastructure. The exchange dictionary is an extension of the macromolecular Crystallographic Information File (mmCIF) data dictionary (Bourne et al., 1997[link]). The dictionary provides the foundation for software tools which exchange and validate data, create and load databases, translate data formats, and serve application program interfaces. The components of the informatics infrastructure developed by the PDB are being used to build a data pipeline to support high-throughput structure determination.

References

Berman, H. M., Henrick, K. & Nakamura, H. (2003). Announcing the worldwide Protein Data Bank. Nature Struct. Biol. 10, 980.
Berman, H. M., Westbrook, J., Feng, Z., Gilliland, G., Bhat, T. N., Weissig, H., Shindyalov, I. N. & Bourne, P. E. (2000). The Protein Data Bank. Nucleic Acids Res. 28, 235–242.
Bernstein, F. C., Koetzle, T. F., Williams, G. J. B., Meyer, E. F. Jr, Brice, M. D., Rodgers, J. R., Kennard, O., Shimanouchi, T. & Tasumi, M. (1977). The Protein Data Bank: a computer-based archival file for macromolecular structures. J. Mol. Biol. 112, 535–542.
Bourne, P. E., Berman, H. M., McMahon, B., Watenpaugh, K. D., Westbrook, J. D. & Fitzgerald, P. M. D. (1997). Macromolecular Crystallographic Information File. Methods Enzymol. 277, 571–590.








































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