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Bioinformatics Advance Access originally published online on October 17, 2006
Bioinformatics 2006 22(24):3101-3102; doi:10.1093/bioinformatics/btl530
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© The Author 2006. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oxfordjournals.org

sGAL: a computational method for finding surface exposed sites in proteins suitable for Cys-mediated cross-linking

G. Andrew Woolley *, En-shiun Lee and Fuzhong Zhang

Department of Chemistry, University of Toronto 80 St. George Street, Toronto, ON M5S 3H6, Canada

*To whom correspondence should be addressed.

sGAL is a computer program designed to find pairs of sites suitable for introducing chemical cross-links into proteins. sGAL takes a protein structure file in PDB format as input, truncates each residue sequentially to its gamma side chain atom to mimic mutation to Cys, and calculates the exposed surface area of the gamma atom. The user then inputs the minimum and maximum lengths of the cross-linker. sGAL provides as output pairs of residues that would have exposed gamma atom separations that fall within this range. Furthermore, if a line joining the pair of gamma atoms contacts more than a given number of buried atoms, that pair is discarded. In this way, sites for which the protein would sterically interfere with cross-linking are avoided.

Availability: http://www.chem.utoronto.ca/staff/GAW/links.html; (Surface Racer is also required see: http://monte.biochem.wisc.edu/~tsodikov/surface.html).

Contact: awoolley{at}chem.utoronto.ca

Received on August 18, 2006; revised on September 25, 2006; accepted on October 10, 2006

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