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Bioinformatics Advance Access published online on March 7, 2006
Bioinformatics, doi:10.1093/bioinformatics/btl079
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© The Author (2006). Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oxfordjournals.org
Received January 20, 2006
Revised February 14, 2006
Accepted February 28, 2006

Article

Predicting protein interaction sites: binding hot-spots in protein-protein and protein-ligand interfaces

Nicholas J. Burgoyne 1 and Richard M. Jackson 1 *

1 Institute of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, LS2 9JT, UK

* To whom correspondence should be addressed.
Richard M. Jackson, E-mail: r.m.jackson{at}leeds.ac.uk


  Abstract

Motivation: Protein assemblies are currently poorly represented in structural databases and their structural elucidation is a key goal in biology. Here we analyse clefts in protein surfaces, likely to correspond to binding "hot-spots", and rank them according to sequence conservation and simple measures of physical properties including hydrophobicity, desolvation, electrostatics and van der Waals energies, to predict which are involved in binding in the native complex.

Results: The resulting differences between predicting binding-sites at protein-protein and protein-ligand interfaces are striking. There is a high level of prediction accuracy (≤93%) for protein-ligand interactions, based on the following attributes: van der Waals potential, electrostatic potential, desolvation and surface conservation. Generally, the prediction accuracy for protein-protein interactions is lower, with the exception of enzymes. Our results show that the ease of cleft desolvation or "de-wetting" is strongly predictive of interfaces and strongly maintained across all classes of protein binding interface.

Associate Editor: Dmitrij Frishman
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