Abstract

Overview and plans for the Protein Data Bank

Biology Dept., Brookhaven National Laboratory, Upton, NY, 11973-5000 USA
Dept. of Structural Biology, Weizmann Institute of Science, 76100 Rehovot, ISRAEL

jls@bnl.gov

The Protein Data Bank (PDB) is an archive of experimentally-determined three dimensional structures of proteins, nucleic acids, and other biological macromolecules which serves a global community of researchers, educators, and students. The challenges presented by the enormous growth in data over the past several years have been met by the PDB staff and management, which now provides an up-to-date archive, while simultaneously expanding network access [1] and building strong world-wide collaborations [2]. Even larger challenges are at hand, as the deposition rate continues to exponentially rise along with the expectations of the consumers of these data. We are enhancing the capabilities of the PDB by transforming it into a new Three-Dimensional Database of Biomacromolecular Structures to store and provide flexible access to the information, while retaining many of the features of the PDB, for compatibility [3]. It uses the SYBASE Relational Database Management System and is constructed with the Object-Protocol Model (OPM), and the OPM data management tools [4].

Over the course of the next few years, we plan to:

• Ensure that the archive remains current, correct, and relevant.
• Provide a rapid and painless automated deposition system, 'AutoDep', using internationally agreed-upon CIF standards.
• Enhance data validation tools.
• Integrate the PDB with complementary biological and chemical databases through semantic links and schema sharing.
• Provide easy access, through the Internet, to the PDB at Brookhaven National Laboratory and other deposition and distribution sites worldwide.

The PDB is supported by a combination of Federal Government Agency funds and user fees. Support is provided by the U.S. National Science Foundation, the U.S. Public Health Service, National Institutes of Health, National Center for Research Resources, National Institutes of General Medical Sciences, National Library of Medicine, and the U.S. Department of Energy under contract DE-AC02-76CH00016.

References:
1. Stampf, D.R., Felder, C.E. & Sussman, J.L. (1995). PDBBrowse - a Graphics Interface to the Brookhaven Protein Data Bank. Nature 374, 572-574.
2. Peitsch, M.C., Stampf, D.R., Wells, T.N.C. & Sussman, J.L. (1995). The Swiss 3D-Image Collection and Brookhaven Protein Data Bank Browser on the World-Wide Web. TIBS 20, 82-84.
3. Abola, E.E., Manning, N.O., Prilusky, J., Stampf, D.R. & Sussman, J.L. (1996). The Protein Data Bank: Current Status and Future Challenges. Journal of Research of the National Institute of Standards and Technology 101, 231-241.
4. Chen, I.A. & Markowitz, V.M. (1995). An Overview of the Object-Protocol Model (OP) and OPM Data Management Tools. Information Systems 20, 393-418.