標題: SiMMap: a web server for inferring site-moiety map to recognize interaction preferences between protein pockets and compound moieties
作者: Chen, Yen-Fu
Hsu, Kai-Cheng
Lin, Shen-Rong
Wang, Wen-Ching
Huang, Yu-Chi
Yang, Jinn-Moon
生物科技學系
生物資訊及系統生物研究所
Department of Biological Science and Technology
Institude of Bioinformatics and Systems Biology
公開日期: 1-七月-2010
摘要: 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 http://simfam.life.nctu.edu.tw/.
URI: http://dx.doi.org/10.1093/nar/gkq480
http://hdl.handle.net/11536/5191
ISSN: 0305-1048
DOI: 10.1093/nar/gkq480
期刊: NUCLEIC ACIDS RESEARCH
Volume: 38
Issue: 
起始頁: W424
結束頁: W430
顯示於類別:期刊論文


文件中的檔案:

  1. 000284148900068.pdf