Work

E asy MIF s and S ite H ound : a toolkit for the identification of ligand-binding sites in protein structures

Year: 2009

Type: article

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.

Source: Bioinformatics

DOI: 10.1093/bioinformatics/btp562

Authors: Dario Ghersi, Roberto Sanchez

Institution: Icahn School of Medicine at Mount Sinai

Language: English

Topic: Computational Drug Discovery Methods

Subfield: Computational Theory and Mathematics

Field: Computer Science

Domain: Physical Sciences

Open Access status: green

Funders: National Science Foundation, National Institutes of Health, National Human Genome Research Institute, National Institute of General Medical Sciences

Awards: Chemical Genomics Paradigm for Epigentic Regulation, G4963949644, High-Accuracy Modeling for Remote Homologues of Known Structures, Genome-Wide Profiling of Protein Module-Ligand Selectivity: A New Structure-based Paradigm