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dc.contributor.authorYuriev, E.
dc.contributor.authorAgostino, Mark
dc.contributor.authorRamsland, P.
dc.date.accessioned2017-01-30T13:51:13Z
dc.date.available2017-01-30T13:51:13Z
dc.date.created2014-09-09T20:01:02Z
dc.date.issued2011
dc.identifier.citationYuriev, E. and Agostino, M. and Ramsland, P. 2011. Challenges and advances in computational docking: 2009 in review. Journal of Molecular Recognition. 24 (2): pp. 149-164.
dc.identifier.urihttp://hdl.handle.net/20.500.11937/35703
dc.identifier.doi10.1002/jmr.1077
dc.description.abstract

Docking is a computational technique that places a small molecule (ligand) in the binding site of its macromolecular target (receptor) and estimates its binding affinity. This review addresses methodological developments that have occurred in the docking field in 2009, with a particular focus on the more difficult, and sometimes controversial, aspects of this promising computational discipline. These developments aim to address the main challenges of docking: receptor representation (such aspects as structural waters, side chain protonation, and, most of all, flexibility (from side chain rotation to domain movement)), ligand representation (protonation, tautomerism and stereoisomerism, and the effect of input conformation), as well as accounting for solvation and entropy of binding. This review is strongly focused on docking advances in the context of drug design, specifically in virtual screening and fragment-based drug design.

dc.publisherJohn Wiley & Sons Ltd.
dc.subjectreceptor flexibility
dc.subjectcomputational docking
dc.subjectbinding mode prediction
dc.subjectprotein-ligand complexes
dc.subjectscoring
dc.titleChallenges and advances in computational docking: 2009 in review
dc.typeJournal Article
dcterms.source.volume24
dcterms.source.startPage149
dcterms.source.endPage164
dcterms.source.issn1099-1352
dcterms.source.titleJournal of Molecular Recognition
curtin.accessStatusFulltext not available


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