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Bioinformatics Advance Access published online on April 26, 2005
Bioinformatics, doi:10.1093/bioinformatics/bti443
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© The Author (2005). Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oupjournals.org
Received February 2, 2005
Revised April 1, 2005
Accepted April 7, 2005

Article

Prediction of protein-protein interactions by combining structure and sequence conservation in protein interfaces

A. Selim Aytuna 1, Attila Gursoy 1*, and Ozlem Keskin 1

1 Koc University, Center for Computational Biology and Bioinformatics, College of Engineering, Rumelifeneri Yolu 34450 Sariyer, Istanbul, Turkey

* To whom correspondence should be addressed.
Attila Gursoy, E-mail: agursoy{at}ku.edu.tr


  Abstract

Motivation: Elucidation of the full network of protein-protein interactions is crucial for understanding of the principles of biological systems and processes; thus there is a need for in silico methods for predicting interactions. We present a novel algorithm for automated prediction of protein-protein interactions that employs a unique bottom-up approach combining structure and sequence conservation in protein interfaces.

Results: Running the algorithm on a template dataset of 67 interfaces and a sequentially non-redundant dataset of 6170 protein structures, 62616 potential interactions are predicted. These interactions are compared with the ones in two publicly available interaction databases (DIP and BIND) and also the PDB. A significant number of predictions are verified in these databases. The unverified ones may correspond to 1) interactions that are not covered in these databases but known in literature 2) unknown interactions that actually occur in nature 3) interactions that do not occur naturally but may possibly be realized synthetically in laboratory conditions. Some unverified interactions, supported significantly with studies found in the literature, are discussed.

Availability: http://gordion.hpc.eng.ku.edu.tr/prism.


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