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Bioinformatics Advance Access originally published online on October 2, 2006
Bioinformatics 2006 22(23):2876-2882; doi:10.1093/bioinformatics/btl490
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© 2006 The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

ProtBuD: a database of biological unit structures of protein families and superfamilies

Qifang Xu 1,2, Adrian Canutescu 1, Zoran Obradovic 2 and Roland L. Dunbrack, Jr 1,*

1 Institute for Cancer Research, Fox Chase Cancer Center 333 Cottman Avenue, Philadelphia PA 19111 USA
2 Center for Information Science and Technology, Temple University 333 Wachman Hall, 1805 N. Broad Street, Philadelphia PA 19122 USA

*To whom correspondence should be addressed.

Motivation: Modeling of protein interactions is often possible from known structures of related complexes. It is often time-consuming to find the most appropriate template. Hypothesized biological units (BUs) often differ from the asymmetric units and it is usually preferable to model from the BUs.

Results: ProtBuD is a database of BUs for all structures in the Protein Data Bank (PDB). We use both the PDBs BUs and those from the Protein Quaternary Server. ProtBuD is searchable by PDB entry, the Structural Classification of Proteins (SCOP) designation or pairs of SCOP designations. The database provides the asymmetric and BU contents of related proteins in the PDB as identified in SCOP and Position-Specific Iterated BLAST (PSI–BLAST). The asymmetric unit is different from PDB and/or Protein Quaternary Server (PQS) BUs for 52% of X-ray structures, and the PDB and PQS BUs disagree on 18% of entries.

Availability: The database is provided as a standalone program and a web server from http://dunbrack.fccc.edu/ProtBuD.php.

Contact: Roland.Dunbrack{at}fccc.edu

Received on May 24, 2006; revised on September 12, 2006; accepted on September 20, 2006

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