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Bioinformatics Advance Access originally published online on October 12, 2007
Bioinformatics 2007 23(24):3397-3399; doi:10.1093/bioinformatics/btm474
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© The Author 2007. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oxfordjournals.org

InterProSurf: a web server for predicting interacting sites on protein surfaces

Surendra S. Negi , Catherine H. Schein , Numan Oezguen , Trevor D. Power and Werner Braun *

Department of Biochemistry and Molecular Biology, Sealy Center for Structural Biology and Molecular Biophysics, University of Texas Medical Branch, Galveston, Texas 77555-0857, USA

*To whom correspondence should be addressed.


  Abstract

Summary: A new web server, InterProSurf, predicts interacting amino acid residues in proteins that are most likely to interact with other proteins, given the 3D structures of subunits of a protein complex. The prediction method is based on solvent accessible surface area of residues in the isolated subunits, a propensity scale for interface residues and a clustering algorithm to identify surface regions with residues of high interface propensities. Here we illustrate the application of InterProSurf to determine which areas of Bacillus anthracis toxins and measles virus hemagglutinin protein interact with their respective cell surface receptors. The computationally predicted regions overlap with those regions previously identified as interface regions by sequence analysis and mutagenesis experiments.

Availability: The InterProSurf web server is available at http://curie.utmb.edu/

Contact: webraun{at}utmb.edu

Supplementary information: Other test examples are available as Supplementary Material at Bioinformatics online.

Associate Editor: Burkhard Rost

Received on July 11, 2007; revised on August 30, 2007; accepted on September 12, 2007

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