ProDGe: investigating protein-protein interactions at the domain level

An important goal of systems biology is the identification and investigation of known and predicted protein-protein interactions to obtain more information about new cellular pathways and processes. Proteins interact via domains, thus it is important to know which domains a protein contains and which domains interact with each other. Here we present the JavaTM program ProDGe (Protein Domain Gene), which visualizes existing and suggests novel domaindomain interactions and protein-protein interactions at the domain level. The comprehensive dataset behind ProDGe consists of protein, domain and interaction information for both layers, collected and combined appropriately from UniProt, Pfam, DOMINE and IntAct. Based on known domain interactions, ProDGe suggests novel protein interactions and assigns them to four confidence classes, depending on the reliability of the underlying domain interaction. Furthermore, ProDGe is able to identify potential homologous interaction partners in other species, which is particularly helpful when investigating poorly annotated species.

Please cite:	Büchel, Finja, Wrzodek, Clemens, Mittag, Florian, Dräger, Andreas, Schröder, Adrian, and Zell, Andreas. ProDGe: investigating protein-protein interactions at the domain level. Available from Nature Precedings <http://dx.doi.org/10.1038/npre.2011.6188.1> (2011)   -   (buechel - 2011-08-04 17:20)
Second Release:	We updated the complete dataset and enhanced the whole application. Click here to get the latest version of ProDGe.   -   (buechel - 2011-05-09 11:58)
Documentation:	A complete documentation is now available.   -   (buechel - 2010-03-01 19:12)
Webstart:	Now ProDGe can be executed as Java webstart.   -   (buechel - 2010-02-22 16:02)
First Release:	Click here to download the application.   -   (buechel - 2008-12-09 16:02)