SiMMap: A web server for inferring site-moiety map to recognize interaction preferences between protein pockets and compound moieties
Nucleic Acids Research, ISSN: 0305-1048, Vol: 38, Issue: SUPPL. 2, Page: W424-30
2010
- 40Citations
- 28Captures
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Example: if you select the 1-year option for an article published in 2019 and a metric category shows 90%, that means that the article or review is performing better than 90% of the other articles/reviews published in that journal in 2019. If you select the 3-year option for the same article published in 2019 and the metric category shows 90%, that means that the article or review is performing better than 90% of the other articles/reviews published in that journal in 2019, 2018 and 2017.
Citation Benchmarking is provided by Scopus and SciVal and is different from the metrics context provided by PlumX Metrics.
Metrics Details
- Citations40
- Citation Indexes40
- 40
- CrossRef17
- Captures28
- Readers28
- 28
Article Description
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/. © The Author(s) 2010. Published by Oxford University Press.
Bibliographic Details
http://www.scopus.com/inward/record.url?partnerID=HzOxMe3b&scp=77954249073&origin=inward; http://dx.doi.org/10.1093/nar/gkq480; http://www.ncbi.nlm.nih.gov/pubmed/20519201; https://academic.oup.com/nar/article-lookup/doi/10.1093/nar/gkq480; https://dx.doi.org/10.1093/nar/gkq480; https://academic.oup.com/nar/article/38/suppl_2/W424/1118579
Oxford University Press (OUP)
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