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Bioinformatics Advance Access originally published online on May 3, 2006
Bioinformatics 2006 22(14):1794-1795; doi:10.1093/bioinformatics/btl171
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© The Author 2006. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oxfordjournals.org

SHARP2: protein–protein interaction predictions using patch analysis

Yoichi Murakami and Susan Jones *

Department of Biochemistry, School of Life Sciences, John Maynard Smith Building, University of Sussex Falmer, Brighton, BN1 9QG, UK

*To whom correspondence should be addressed.

Summary: SHARP2 is a flexible web-based bioinformatics tool for predicting potential protein–protein interaction sites on protein structures. It implements a predictive algorithm that calculates multiple parameters for overlapping patches of residues on the surface of a protein. Six parameters are calculated: solvation potential, hydrophobicity, accessible surface area, residue interface propensity, planarity and protrusion (SHARP2). Parameter scores for each patch are combined, and the patch with the highest combined score is predicted as a potential interaction site. SHARP2 enables users to upload 3D protein structure files in PDB format, to obtain information on potential interaction sites as downloadable HTML tables and to view the location of the sites on the 3D structure using Jmol. The server allows for the input of multiple structures and multiple combinations of parameters. Therefore predictions can be made for complete datasets, as well as individual structures.

Availability: http://www.bioinformatics.sussex.ac.uk/SHARP2

Contact: s.jones{at}sussex.ac.uk

Received on April 6, 2006; accepted on April 27, 2006

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