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Bioinformatics Advance Access originally published online on February 15, 2005
Bioinformatics 2005 21(10):2534-2536; doi:10.1093/bioinformatics/bti322
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© The Author 2005. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions{at}oupjournals.org

FastContact: rapid estimate of contact and binding free energies

Carlos J. Camacho 1,* and Chao Zhang 2

1Department of Computational Biology, University of Pittsburgh Pittsburgh, PA 15261, USA
2Plexxikon Inc. 91 Bolivar Drive, Berkeley, CA 94710, USA

*To whom correspondence should be addressed.

Summary: Interaction free energies are crucial for analyzing binding propensities in proteins. Although the problem of computing binding free energies remains open, approximate estimates have become very useful for filtering potential binding complexes. We report on the implementation of a fast computational estimate of the binding free energy based on a statistically determined desolvation contact potential and Coulomb electrostatics with a distance-dependent dielectric constant, and validated in the Critical Assessment of PRotein Interactions experiment. The application also reports residue contact free energies that rapidly highlight the hotspots of the interaction.

Availability: The program was written in Fortran. The executable and full documentation is freely available at http://structure.pitt.edu/software/FastContact

Contact: ccamacho{at}pitt.edu


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