Assessing protein-ligand binding modes with computational tools: the case of PDE4B

dc.contributor.authorÇifii, Gülşah
dc.contributor.authorAviyente, Viktorya
dc.contributor.authorAkten, Ebru Demet
dc.contributor.authorMonard, Gerald
dc.date.accessioned2019-06-27T08:01:19Z
dc.date.available2019-06-27T08:01:19Z
dc.date.issued2017
dc.departmentFakülteler, Mühendislik ve Doğa Bilimleri Fakültesi, Biyoinformatik ve Genetik Bölümüen_US
dc.description.abstractIn a first step in the discovery of novel potent inhibitor structures for the PDE4B family with limited side effects we present a protocol to rank newly designed molecules through the estimation of their IC values. Our protocol is based on reproducing the linear relationship between the logarithm of experimental IC values [(IC)] and their calculated binding free energies (). From 13 known PDE4B inhibitors we show here that (1) binding free energies obtained after a docking process by AutoDock are not accurate enough to reproduce this linear relationshipen_US]
dc.description.abstract(2) MM-GB/SA post-processing of molecular dynamics (MD) trajectories of the top ranked AutoDock pose improves the linear relationshipen_US]
dc.description.abstract(3) by taking into account all representative structures obtained by AutoDock and by averaging MM-GB/SA computations on a series of 40 independent MD trajectories a linear relationship between (IC) and the lowest is achieved with R-2 = 0.944 .en_US]
dc.identifier.citation1
dc.identifier.doi10.1007/s10822-017-0024-7en_US
dc.identifier.endpage575
dc.identifier.issn0920-654Xen_US
dc.identifier.issn1573-4951en_US
dc.identifier.issn0920-654X
dc.identifier.issn1573-4951
dc.identifier.issue6
dc.identifier.pmid28534194en_US
dc.identifier.scopus2-s2.0-85019924963en_US
dc.identifier.scopusqualityQ2
dc.identifier.startpage563en_US
dc.identifier.urihttps://hdl.handle.net/20.500.12469/341
dc.identifier.urihttps://doi.org/10.1007/s10822-017-0024-7
dc.identifier.volume31en_US
dc.identifier.wosWOS:000403689700004en_US
dc.identifier.wosqualityQ2
dc.institutionauthorAkten, Ebru Demeten_US
dc.language.isoenen_US
dc.publisherSpringeren_US
dc.relation.journalJournal of Computer-Aided Molecular Designen_US
dc.relation.publicationcategoryMakale - Uluslararası Hakemli Dergi - Kurum Öğretim Elemanıen_US
dc.rightsinfo:eu-repo/semantics/openAccessen_US
dc.subjectPDE4Ben_US
dc.subjectIC50en_US
dc.subjectMolecular dockingen_US
dc.subjectMolecular dynamicsen_US
dc.subjectMM-GB/SAen_US
dc.titleAssessing protein-ligand binding modes with computational tools: the case of PDE4Ben_US
dc.typeArticleen_US
dspace.entity.typePublication

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