1. SITEHOUND-web: a server for ligand binding site identification in protein structures
- Author
-
Dario Ghersi, Roberto Sanchez, and Marylens Hernandez
- Subjects
Protein Conformation ,Interactive 3d ,Protein Data Bank (RCSB PDB) ,information science ,Computational biology ,Biology ,Bioinformatics ,computer.software_genre ,Ligands ,03 medical and health sciences ,User-Computer Interface ,Protein structure ,Genetics ,natural sciences ,Binding site ,Java applet ,030304 developmental biology ,0303 health sciences ,Internet ,Binding Sites ,Extramural ,030302 biochemistry & molecular biology ,A protein ,Articles ,Identification (information) ,computer ,Algorithms ,Software - Abstract
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.
- Published
- 2009