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dc.contributor.authorKotev, Martin
dc.contributor.authorSoliva, Robert
dc.contributor.authorOrozco, Modesto
dc.contributor.otherBarcelona Supercomputing Center
dc.date.accessioned2016-10-20T09:31:41Z
dc.date.available2018-10-16T00:30:47Z
dc.date.issued2016-10-15
dc.identifier.citationKotev, Martin; Soliva, Robert; Orozco, Modesto. Challenges of docking in large, flexible and promiscuous binding sites. "Bioorganic & Medicinal Chemistry", 15 Octubre 2016, vol. 24, núm. 20, p. 4961-4969.
dc.identifier.issn0968-0896
dc.identifier.urihttp://hdl.handle.net/2117/90906
dc.description.abstractAfter decades of work, the correct determination of the binding mode of a small molecule into a target protein is still a challenging problem, whose difficulty depends on: (i) the sizes of the binding site and the ligand; (ii) the flexibility of both interacting partners, and (iii) the differential solvation of bound and unbound partners. We have evaluated the performance of standard rigid(receptor)/flexible(ligand) docking approaches with respect to last-generation fully flexible docking methods to obtain reasonable poses in a very challenging case: soluble Epoxide Hydrolase (sEH), a flexible protein showing different binding sites. We found that full description of the flexibility of both protein and ligand and accurate description of solvation leads to significant improvement in the ability of docking to reproduce well known binding modes, and at the same time capture the intrinsic binding promiscuity of the protein.
dc.format.extent9 p.
dc.language.isoeng
dc.publisherElsevier
dc.subjectÀrees temàtiques de la UPC::Enginyeria biomèdica
dc.subject.lcshProtein binding
dc.subject.lcshSimulations
dc.subject.otherInduced-fit docking
dc.subject.otherPELE simulations
dc.subject.otherSoluble Epoxide Hydrolase
dc.subject.otherBenchmark
dc.titleChallenges of docking in large, flexible and promiscuous binding sites
dc.typeArticle
dc.subject.lemacProteïnes--Investigació
dc.subject.lemacSimulació, Mètodes de
dc.identifier.doi10.1016/j.bmc.2016.08.010
dc.description.peerreviewedPeer Reviewed
dc.relation.publisherversionhttp://www.sciencedirect.com/science/article/pii/S0968089616306022
dc.rights.accessOpen Access
dc.description.versionPostprint (author's final draft)
dc.relation.projectidinfo:eu-repo/grantAgreement/MINECO//BIO2015-64802-R/ES/ESTUDIO DE FORMAS INUSUALES Y TENSIONADAS DE LOS ACIDOS NUCLEICOS DE INTERES BIOMEDICO Y BIOTECNOLOGICO./
dc.relation.projectidinfo:eu-repo/grantAgreement/EC/H2020/675728/EU/Centre of Excellence for Biomolecular Research/BioExcel
local.citation.publicationNameBioorganic & Medicinal Chemistry
local.citation.volume24
local.citation.number20
local.citation.startingPage4961
local.citation.endingPage4969


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