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

Andrew G. Woolley, En shiun Lee, Fuzhong Zhang

Research output: Contribution to journalArticlepeer-review

11 Scopus citations

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.

Original languageEnglish
Pages (from-to)3101-3102
Number of pages2
JournalBioinformatics
Volume22
Issue number24
DOIs
StatePublished - Dec 15 2006

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