SiMMap: a web server for inferring site-moiety map to recognize interaction preferences between protein pockets and compound moieties.

ABSTRACT: The protein-ligand interacting mechanism is essential to biological processes and drug discovery. The SiMMap server statistically derives site-moiety map with several anchors, which describe the relationship between the moiety preferences and physico-chemical properties of the binding site, from the interaction profiles between query target protein and its docked (or co-crystallized) compounds. Each anchor includes three basic elements: a binding pocket with conserved interacting residues, the moiety composition of query compounds and pocket-moiety interaction type (electrostatic, hydrogen bonding or van der Waals). We provide initial validation of the site-moiety map on three targets, thymidine kinase, and estrogen receptors of antagonists and agonists. Experimental results show that an a

SUBMITTER: Chen YF 

PROVIDER: S-EPMC2896162 | biostudies-literature | 2010 Jul

REPOSITORIES: biostudies-literature