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Bioinformatics Advance Access published online on October 17, 2006
Bioinformatics, 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
Received August 18, 2006
Revised September 25, 2006
Accepted October 10, 2006

Applications note

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

G. Andrew Woolley 1 *, En-shiun Lee 1, and Fuzhong Zhang 1

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

* To whom correspondence should be addressed.
G. Andrew Woolley, E-mail: awoolley{at}chem.utoronto.ca


  Abstract

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).

Associate Editor: Anna Tramontano
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