Nuclc. Acids. Res. OUP
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PDB

http://www.rcsb.org/pdb/

Contact   berman@rcsb.rutgers.edu


Database Description

The Protein Data Bank (PDB; http://www.rcsb.org/pdb/ and http://www.bnl.org/) is the single worldwide archive of structural data of biological macromolecules. A description of the architecture and functionality of the systems used to collect, archive, distribute, and query the data were described previously (Berman et al., Nucleic Acids Research, 28 pp. 235-242 (2000)). The PDB Web sites provide users with direct query and reporting capabilities using the underlying databases. The query capabilities are quite extensive. Query across the complete PDB has nevertheless been limited by missing, erroneous, and inconsistently reported experimental data, nomenclature, and functional annotation. Inconsistency, in particular, reflects the evolution of experimental methods, functional knowledge of proteins, and methods used to process these data over the years. This paper describes how the PDB is addressing these problems by re-examining individual families of proteins (file-by-file) and individual records present for every structure in the archive (record-by-record). The initial results of this effort from the perspective of a user querying the PDB are given.

Category   Structure

Go to the abstract in the NAR 2002 Database Issue.

 

Compilation Paper
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