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

Yen Fu Chen, Kai Cheng Hsu, Shen Rong Lin, Wen Ching Wang, Yu Chi Huang, Jinn Moon Yang

Research output: Contribution to journalArticle

27 Citations (Scopus)


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 physicochemical 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 anchor is often a hot spot and the site-moiety map can help to assemble potential leads by optimal steric, hydrogen bonding and electronic moieties. When a compound highly agrees with anchors of site-moiety map, this compound often activates or inhibits the target protein. We believe that the site-moiety map is useful for drug discovery and understanding biological mechanisms. The SiMMap web server is available at

Original languageEnglish
Article numbergkq480
JournalNucleic Acids Research
Issue numberSUPPL. 2
Publication statusPublished - Jun 2 2010
Externally publishedYes


ASJC Scopus subject areas

  • Genetics
  • Medicine(all)

Cite this