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Open Access Method

InSite: a computational method for identifying protein-protein interaction binding sites on a proteome-wide scale

Haidong Wang1, Eran Segal2, Asa Ben-Hur3, Qian-Ru Li4, Marc Vidal4 and Daphne Koller1*

Author Affiliations

1 Computer Science Department, Stanford University, Serra Mall, Stanford, CA 94305, USA

2 Department of Computer Science and Applied Mathematics, Weizmann Institute of Science, Rehovot 76100, Israel

3 Computer Science Department, Colorado State University, South Howes Street, Fort Collins, CO 80523, USA

4 Center for Cancer Systems Biology (CCSB) and Department of Cancer Biology, Dana-Farber Cancer Institute, and Department of Genetics, Harvard Medical School, Binney Street, Boston, MA 02115, USA

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Genome Biology 2007, 8:R192  doi:10.1186/gb-2007-8-9-r192

Published: 14 September 2007

Abstract

We propose InSite, a computational method that integrates high-throughput protein and sequence data to infer the specific binding regions of interacting protein pairs. We compared our predictions with binding sites in Protein Data Bank and found significantly more binding events occur at sites we predicted. Several regions containing disease-causing mutations or cancer polymorphisms in human are predicted to be binding for protein pairs related to the disease, which suggests novel mechanistic hypotheses for several diseases.