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Bioinformatics Advance Access originally published online on September 29, 2009
Bioinformatics 2009 25(23):3185-3186; doi:10.1093/bioinformatics/btp562
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© The Author 2009. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oxfordjournals.org

EASYMIFS and SITEHOUND: a toolkit for the identification of ligand-binding sites in protein structures

Dario Ghersi and Roberto Sanchez *

Department of Structural and Chemical Biology, Mount Sinai School of Medicine, 1425 Madison Avenue, New York, NY 10029, USA

* To whom correspondence should be addressed.


  Abstract

Summary: SITEHOUND uses Molecular Interaction Fields (MIFs) produced by EASYMIFS to identify protein structure regions that show a high propensity for interaction with ligands. The type of binding site identified depends on the probe atom used in the MIF calculation. The input to EASYMIFS is a PDB file of a protein structure; the output MIF serves as input to SITEHOUND, which in turn produces a list of putative binding sites. Extensive testing of SITEHOUND for the detection of binding sites for drug-like molecules and phosphorylated ligands has been carried out.

Availability: EASYMIFS and SITEHOUND executables for Linux, Mac OS X, and MS Windows operating systems are freely available for download from http://sitehound.sanchezlab.org/download.html.

Contact: roberto{at}sanchezlab.org or roberto.sanchez{at}mssm.edu

Supplementary information: Supplementary data are available at Bioinformatics online.

Associate Editor: Burkhard Rost

Received on March 12, 2009; revised on September 4, 2009; accepted on September 25, 2009

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