|
International
Tables for Crystallography Volume F Crystallography of biological macromolecules Edited by M. G. Rossmann and E. Arnold © International Union of Crystallography 2006 |
International Tables for Crystallography (2006). Vol. F. ch. 24.5, p. 675
Section 24.5.1. Introduction
H. M. Berman,a* J. Westbrook,a Z. Feng,a G. Gilliland,b T. N. Bhat,b H. Weissig,c I. N. Shindyalovc and P. E. Bourned
a
Department of Chemistry, Rutgers University, 610 Taylor Road, Piscataway, NJ 08854-8087, USA,bNational Institute of Standards and Technology, Biotechnology Division, 100 Bureau Drive, Gaithersburg, MD 20899, USA,cSan Diego Supercomputer Center, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0537, USA, and dDepartment of Pharmacology, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0537, USA |
The Protein Data Bank (PDB) was established at Brookhaven National Laboratory (BNL) (Bernstein et al., 1977![[link]](/graphics/greenarr.gif)
) in 1971 as an archive for biological macromolecular crystal structures. In the beginning there were seven structures, and each year a handful more were deposited. In the 1980s the number of deposited structures began to increase dramatically. This was due to the improved technology for all aspects of the crystallographic process, the addition of structures determined by nuclear magnetic resonance (NMR) methods and changes in the community views about data sharing. By the early 1990s the majority of journals required a PDB accession code and at least one funding agency (National Institute of General Medical Sciences) adopted the guidelines published by the IUCr requiring data deposition for all structures.
The mode of access to PDB data has changed over the years as a result of improved technology, notably the availability of the World Wide Web (WWW) replacing distribution solely via magnetic media. Further, the need to analyse diverse data sets required the development of modern data-management systems.
Initial use of the PDB had been limited to a small group of experts involved in structural research. Today depositors to the PDB have varying expertise in the techniques of X-ray crystal-structure determination, NMR, cryoelectron microscopy and theoretical modelling. Users are a very diverse group of researchers in biology and chemistry, community scientists, educators and students at all levels. The tremendous influx of data soon to be fuelled by the structural genomics initiative, and the increased recognition of the value of the data toward understanding biological function, demand new ways to collect, organize and distribute the data.
The vision of the Research Collaboratory for Structural Bioinformatics (RCSB)1 is to create a resource based on the most modern technology that would facilitate the use and analysis of structural data and thus create an enabling resource for biological research. In October 1998, the management of the PDB became the responsibility of the RCSB.2 In this chapter, we describe the current procedures for deposition, processing and distribution of PDB data by the RCSB. We conclude with some current developments of the PDB.
References
Bernstein, F. C., Koetzle, T. F., Williams, G. J., Meyer, E. E., Brice, M. D., Rodgers, J. R., Kennard, O., Shimanouchi, T. & Tasumi, M. (1977). Protein Data Bank: a computer-based archival file for macromolecular structures. J. Mol. Biol. 112, 535–542.Google Scholar
