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Bioinformatics Advance Access published online on May 3, 2006
Bioinformatics, 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
Received April 6, 2006
Accepted April 27, 2006

Applications note

SHARP2: protein-protein interaction predictions using patch analysis

Yoichi Murakami 1 and Susan Jones 1 *

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

* To whom correspondence should be addressed.
Susan Jones, E-mail: s.jones{at}sussex.ac.uk


  Abstract

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 3-D protein structure files in PDB format, and obtain information on potential interaction sites as downloadable HTML tables, and 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, so predictions can be made for complete datasets, as well as individual structures.

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

Associate Editor: Martin Bishop
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