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Bioinformatics Advance Access originally published online on October 28, 2004
Bioinformatics 2005 21(6):827-828; doi:10.1093/bioinformatics/bti098
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© The Author 2004. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions{at}oupjournals.org

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

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

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

*To whom correspondence should be addressed.

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.

Contact: pdzbase{at}med.cornell.edu.


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