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Nucleic Acids Research Advance Access originally published online on May 30, 2007
Nucleic Acids Research 2007 35(Web Server issue):W556-W560; doi:10.1093/nar/gkm326
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Nucleic Acids Research, 2007, Vol. 35, No. suppl_2 W556-W560
© 2007 The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

Articles

FastContact: a free energy scoring tool for protein–protein complex structures

P. Christoph Champ and Carlos J. Camacho*

Department of Computational Biology, University of Pittsburgh, Pittsburgh, PA, USA

*To whom correspondence should be addressed. Tel: +4126487776; Email: ccamacho{at}pitt.edu

Received January 31, 2007. Revised March 23, 2007. Accepted April 17, 2007.

‘FastContact’ is a server that estimates the direct electrostatic and desolvation interaction free energy between two proteins in units of kcal/mol. Users submit two proteins in PDB format, and the output is emailed back to the user in three files: one output file, and the two processed proteins. Besides the electrostatic and desolvation free energy, the server reports residue contact free energies that rapidly highlight the hotspots of the interaction and evaluates the van der Waals interaction using CHARMm. Response time is ~1 min. The server has been successfully tested and validated, scoring refined complex structures and blind sets of docking decoys, as well as proven useful predicting protein interactions. ‘FastContact’ offers unique capabilities from biophysical insights to scoring and identifying important contacts.


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