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Nucleic Acids Research Advance Access originally published online on April 26, 2009
Nucleic Acids Research 2009 37(Web Server issue):W413-W416; doi:10.1093/nar/gkp281
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Nucleic Acids Research, 2009, Vol. 37, No. suppl_2 W413-W416
© 2009 The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

Articles

SITEHOUND-web: a server for ligand binding site identification in protein structures

Marylens Hernandez, Dario Ghersi and Roberto Sanchez*

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

*To whom correspondence should be addressed. Tel: +1 212 659 8648; Fax: +1 212 659 8232; Email: roberto{at}sanchezlab.org or roberto.sanchez{at}mssm.edu

Received March 1, 2009. Revised April 6, 2009. Accepted April 14, 2009.

SITEHOUND-web (http://sitehound.sanchezlab.org) is a binding-site identification server powered by the SITEHOUND program. Given a protein structure in PDB format SITEHOUND-web will identify regions of the protein characterized by favorable interactions with a probe molecule. These regions correspond to putative ligand binding sites. Depending on the probe used in the calculation, sites with preference for different ligands will be identified. Currently, a carbon probe for identification of binding sites for drug-like molecules, and a phosphate probe for phosphorylated ligands (ATP, phoshopeptides, etc.) have been implemented. SITEHOUND-web will display the results in HTML pages including an interactive 3D representation of the protein structure and the putative sites using the Jmol java applet. Various downloadable data files are also provided for offline data analysis.


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