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Bioinformatics Advance Access published online on May 27, 2005
Bioinformatics, doi:10.1093/bioinformatics/bti520
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© The Author (2005). Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oupjournals.org
Received January 18, 2005
Revised May 10, 2005
Accepted May 25, 2005

Applications note

COREX/BEST Server: a web browser-based program that calculates regional stability variations within protein structures

Jason Vertrees 1, Phillip Barritt 2, Steve Whitten 2, and Vincent J. Hilser 2*

1 Department of Human Biological Chemistry & Genetics, and Sealy Center for Structural Biology, University of Texas Medical Branch at Galveston, TX USA 77555; Houston Area Molecular Biophysics Program (HAMPB) Pre-doctoral Fellow
2 Department of Human Biological Chemistry & Genetics, and Sealy Center for Structural Biology, University of Texas Medical Branch at Galveston, TX USA 77555

* To whom correspondence should be addressed.
Vincent J. Hilser, E-mail: vjhilser{at}utmb.edu


  Abstract

Utilizing the user-supplied coordinates of a protein structure, the COREX/BEST Server generates a structural thermodynamic ensemble. This conformational ensemble can then be used to calculate the regional variations in stability of a protein structure, and the stabilities are presented in units of energy (kcal/mol). The regional stabilities, which are calculated at the resolution of individual residues, can be mapped onto the protein structure for visual representation and downloaded from the site in the form of tab delimited text. The site provides an easy to follow summary of the theoretical and algorithmic approaches and provides links to references for more detailed descriptions.

Availability: The COREX/BEST Server may be accessed through a typical web browser by visiting http://best.utmb.edu/.


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