institute for computational biomedicine: PDZBase

[ description ]

PDZBase is a database aimed at the assembly of all known PDZ-domain mediated protein-protein interactions. PDZBase currently contains 339 interactions, which have been manually extracted from >200 articles. All interactions satisfy the following criteria:

All interactions included in PDZBase are mediated directly by the PDZ-domain, and not by any other possible domain within the protein.

In vivo (co-immunoprecipitation) or in vitro experiments (GST-fusion or related pull-down experiments) have to be used to identify the interaction, and interactions shown only through high throughput methods (e.g., yeast two-hybrid or mass spectrometry) have not been included in PDZBase.

Interactions have only been included when knowledge of the binding-sites on both interacting proteins is available (for instance through a truncation or mutagenesis experiment).

[ about the method ]

PDZBase: A protein-protein interaction database for PDZ-domains. Thijs Beuming, Lucy Skrabanek, Masha Y. Niv, Piali Mukherjee and Harel Weinstein. (2004) Bioinformatics. Accepted for publication.

[ documentation ]

Visit the following help pages for more information about PDZBase:

Accessing PDZBase

Generic Numbering of PDZ domains

RBDG-Diagrams of PDZ domains

Sequence Motif Queries

Exporting from PDZBase

[ availability ]

PDZBase home page: [ access PDZBase ]

If you have questions or comments about PDZbase, you can e-mail us at: pdzbase@med.cornell.edu

News

Jul, 2009; ChIPseeqer, a comprehensive framework for analysis of ChIP-seq data developed in the Elemento lab, is now available for download. [More]
Apr, 2009; The BDVal program developed by the Campagne laboratory for MAQC-II is now available from http://bdval.org. The software supports the development and evaluation of predictive biomarker models from high-throughput data. The web site offers binary and source distributions. [More]
Jan, 2009; Twease now supports searching MEDLINE articles by Author, Journal, and Publication Year. Examples for performing these searches can be found in the updated Twease tutorial. [More]

[News Archives] [Mailing List]

Events

Dec 11th; 4:00pm-5:00pm: Institute for Computational Biomedicine Research in Progress Seminar Series - Fabien Campagne; ICB Conference Room - Y.1301
Jan 15th; 4:00pm-5:00pm: Institute for Computational Biomedicine Research in Progress Seminar Series - Lei Shi; ICB Conference Room - Y.1301
Feb 12th; 4:00pm-5:00pm: Institute for Computational Biomedicine Research in Progress Seminar Series - Christopher E. Mason; ICB Conference Room - Y.1301
Mar 12th; 4:00pm-5:00pm: Institute for Computational Biomedicine Research in Progress Seminar Series - Olivier Elemento; ICB Conference Room - Y.1301
Apr 9th; 4:00pm-5:00pm: Institute for Computational Biomedicine Research in Progress Seminar Series - Emre Aksay; ICB Conference Room - Y.1301
May 14th; 4:00pm-5:00pm: Institute for Computational Biomedicine Research in Progress Seminar Series - Jonathan D. Victor; ICB Conference Room - Y.1301
Jun 11th; 4:00pm-5:00pm: Institute for Computational Biomedicine Research in Progress Seminar Series - Harel Weinstein; ICB Conference Room - Y.1301
Jul 9th; 4:00pm-5:00pm: Institute for Computational Biomedicine Research in Progress Seminar Series - Duane Hassane; ICB Conference Room - Y.1301