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EasyMIFS and SiteHound: a toolkit for the identification of ligand-binding sites in protein structures.

ABSTRACT:

Unlabelled

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.

Supplementary information

Supplementary data are available at Bioinformatics online.

SUBMITTER: Ghersi D

PROVIDER: S-EPMC2913663 | biostudies-literature | 2009 Dec

REPOSITORIES: biostudies-literature

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EasyMIFS and SiteHound: a toolkit for the identification of ligand-binding sites in protein structures.

Ghersi Dario D Sanchez Roberto R

Bioinformatics (Oxford, England) 20090929 23

<h4>Unlabelled</h4>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 ...[more]

PMID: 19789268

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