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Bioinformatics Advance Access published online on February 22, 2005
Bioinformatics, doi:10.1093/bioinformatics/bti340
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© The Author (2005). Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oupjournals.org
Received December 31, 2004
Accepted February 17, 2005

Article

An evolution based classifier for prediction of protein interfaces without using protein structures

I. Res 1, I. Mihalek 1, and O. Lichtarge 1*

1 Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030

* To whom correspondence should be addressed.
O. Lichtarge, E-mail: lichtarge{at}bcm.tmc.edu


  Abstract

Motivation: The number of available protein structures still lags far behind the number of known protein sequences. This makes it important to predict which residues participate in protein-protein interactions using only sequence information. Few studies have tackled this problem until now.

Results: Here, we applied support vector machines (SVMs) to sequences in order to generate a classification of all protein residues into those that are part of a protein interface and those that are not. For the first time evolutionary information was used as one of the attributes and this inclusion of evolutionary importance rankings improves the classification. Leave-one-out cross-validation experiments show that prediction accuracy reaches 64%.


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