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Bioinformatics Advance Access published online on October 2, 2006
Bioinformatics, doi:10.1093/bioinformatics/btl490
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© 2006 The Author(s)
Received May 24, 2006
Revised September 12, 2006
Accepted September 20, 2006

Article

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

Qifang Xu 1, Adrian Canutescu 2, Zoran Obradovic 3, and Roland L. Dunbrack Jr. 2 *

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

* To whom correspondence should be addressed.
Roland L. Dunbrack Jr., E-mail: Roland.Dunbrack{at}fccc.edu


  Abstract

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 often differ from the asymmetric units, and it is usually preferable to model from the biological units.

Results: ProtBuD is a database of biological units for all structures in the PDB. We use both the PDB's biological units and those from the Protein Quaternary Server. ProtBuD is searchable by PDB entry, SCOP designation, or pairs of SCOP designations. The database provides the asymmetric and biological unit contents of related proteins in the PDB as identified in SCOP and PSI-BLAST. The asymmetric unit is different from PDB and/or PQS biological units for 52% of X-ray structures, and the PDB and PQS biological units 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.

Associate Editor: Thomas Lengauer
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