DDI2PPI: an integrated web server for protein-protein interaction and residue contact matrix predictions

Protein-protein interactions (PPIs) play essential roles in many biological processes. The large gap between the fast growing protein sequence information and the experimentally verified PPI information has motivated the development of computational methods to predict PPIs and residue-residue (RR) contacts. Although many tools are available for PPI predictions, most do not make a distinction between direct PPIs, which refer to physical contacts between two proteins, and indirect PPIs. Furthermore, few tools predict detailed RR contacts between interacting proteins, which are valuable for understanding chemical interaction mechanisms and designing investigations of the interaction. Here we present the web server DDI2PPI to provide PPI and RR contact matrix predictions from query protein sequences, focusing on predicting direct physical interactions. DDI2PPI implements algorithms that predict PPIs and RR contact matrices through domain-domain interaction (DDI) analysis based on interaction profile Hidden Markov Models (ipHMMs) and Support Vector Machines (SVMs). It covers more than 6000 DDI families in 3DID, a database of three-dimensional interacting domains. DDI2PPI (version 1.0) is freely available at http://annotation.dbi.udel.edu/ppi_prediction/.