The Protein Data Bank: Current Status and Future Challenges

The Protein Data Bank (PDB) is an archive of experimentally determined three-dimensional structures of proteins, nucleic acids, and other biological macromolecules with a 25 year history of service to a global community. PDB is being replaced by 3DB, the Three-Dimensional Database of Biomolecular Structures that will continue to operate from Brookhaven National Laboratory. 3DB will be a highly sophisticated knowledge-based system for archiving and accessing structural information that combines the advantages of object oriented and relational database systems. 3DB will operate as a direct-deposition archive that will also accept third-party supplied annotations. Conversion of PDB to 3DB will be evolutionary, providing a high degree of compatibility with existing software.

[1]  A. Bairoch.  The ENZYME data bank. , 1993, Nucleic acids research.

[2]  D. Lipman,et al.  Improved tools for biological sequence comparison. , 1988, Proceedings of the National Academy of Sciences of the United States of America.

[3]  I-Min A Chen,et al.  An Overview of the Object-Protocol Model (OPM) and OPM Data Management Tools , 1995, Inf. Syst..

[4]  Kathryn E. Sidman,et al.  The protein identification resource (PIR). , 1986, Nucleic acids research.

[5]  Joel L Sussman,et al.  PDBBrowse — a graphics interface to the Brookhaven Protein Data Bank , 1995, Nature.

[6]  A. Bairoch,et al.  PROSITE: recent developments. , 1994, Nucleic acids research.

[7]  Claude Liébecq.  Biochemical nomenclature and related documents : a compendium , 1992 .

[8]  W. M. Westler,et al.  A relational database for sequence-specific protein NMR data , 1991, Journal of biomolecular NMR.

[9]  K. Nishikawa,et al.  Constructing a protein mutant database. , 1994, Protein engineering.

[10]  L. Brooke.  The National Library of Medicine. , 1980, Hospital libraries.

[11]  A. Bairoch,et al.  The SWISS-PROT protein sequence data bank: current status. , 1994, Nucleic acids research.

[12]  F. Allen,et al.  The crystallographic information file (CIF) : a new standard archive file for crystallography , 1991 .

[13]  G J Williams,et al.  The Protein Data Bank: a computer-based archival file for macromolecular structures. , 1978, Archives of biochemistry and biophysics.

[14]  W. Raub.  From the National Institutes of Health. , 1990, JAMA.

[15]  K. H. Fasman,et al.  The GDB Human Genome Data Base anno 1994. , 1994, Nucleic acids research.

[16]  S. Henikoff,et al.  Protein family classification based on searching a database of blocks. , 1994, Genomics.

[17]  Hans-Werner Mewes,et al.  The PIR-International Protein Sequence Database , 1992, Nucleic Acids Res..

[18]  Axel T. Brunger,et al.  X-PLOR Version 3.1: A System for X-ray Crystallography and NMR , 1992 .

[19]  E. Myers,et al.  Basic local alignment search tool. , 1990, Journal of molecular biology.

[20]  Owen Johnson,et al.  The development of versions 3 and 4 of the Cambridge Structural Database System , 1991, J. Chem. Inf. Comput. Sci..

[21]  M C Peitsch,et al.  The Swiss-3DImage collection and PDB-Browser on the World-Wide Web. , 1995, Trends in biochemical sciences.