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Bioinformatics Advance Access published online on October 28, 2004
Bioinformatics, doi:10.1093/bioinformatics/bti098
Bioinformatics © Oxford University Press 2004; all rights reserved
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Received August 14, 2004
Revised October 5, 2004
Accepted October 8, 2004

Applications note

PDZBase: a protein-protein interaction database for PDZ-domains

Thijs Beuming 1, Lucy Skrabanek 2, Masha Y. Niv 1, Piali Mukherjee 3, and Harel Weinstein 2*

1 Department of Physiology and Biophysics, Weill Medical College of Cornell University, 1300 York Ave., New York, NY 10021
2 Department of Physiology and Biophysics, Weill Medical College of Cornell University, 1300 York Ave., New York, NY 10021; Institute for Computational Biomedicine, Weill Medical College of Cornell University, 1300 York Ave., New York, NY 10021
3 Institute for Computational Biomedicine, Weill Medical College of Cornell University, 1300 York Ave., New York, NY 10021

* To whom correspondence should be addressed.
Harel Weinstein, E-mail: pdzbase{at}med.cornell.edu


  Abstract

Summary: PDZBase is a database that aims to contain all known PDZ-domain mediated protein-protein interactions. Currently, PDZBase contains approximately 300 such interactions, which have been manually extracted from >200 articles. The database can be queried through both sequence motif and keyword-based searches, and the sequences of interacting proteins can be visually inspected through alignments (for the comparison of several interactions), or as residue based diagrams including schematic secondary structure information (for individual complexes).

Availability: http://icb.med.cornell.edu/services/pdz/start.


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