Assessing Protein-Ligand Binding Modes With Computational Tools: the Case of Pde4b

dc.contributor.author Çifii, Gülşah
dc.contributor.author Akdoğan, Ebru Demet
dc.contributor.author Aviyente, Viktorya
dc.contributor.author Akten, Ebru Demet
dc.contributor.author Monard, Gerald
dc.contributor.other Molecular Biology and Genetics
dc.date.accessioned 2019-06-27T08:01:19Z
dc.date.available 2019-06-27T08:01:19Z
dc.date.issued 2017
dc.department Fakülteler, Mühendislik ve Doğa Bilimleri Fakültesi, Biyoinformatik ve Genetik Bölümü en_US
dc.description.abstract In 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 relationship en_US]
dc.description.abstract (2) MM-GB/SA post-processing of molecular dynamics (MD) trajectories of the top ranked AutoDock pose improves the linear relationship en_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.citationcount 1
dc.identifier.doi 10.1007/s10822-017-0024-7 en_US
dc.identifier.endpage 575
dc.identifier.issn 0920-654X en_US
dc.identifier.issn 1573-4951 en_US
dc.identifier.issn 0920-654X
dc.identifier.issn 1573-4951
dc.identifier.issue 6
dc.identifier.pmid 28534194 en_US
dc.identifier.scopus 2-s2.0-85019924963 en_US
dc.identifier.scopusquality Q2
dc.identifier.startpage 563 en_US
dc.identifier.uri https://hdl.handle.net/20.500.12469/341
dc.identifier.uri https://doi.org/10.1007/s10822-017-0024-7
dc.identifier.volume 31 en_US
dc.identifier.wos WOS:000403689700004 en_US
dc.identifier.wosquality Q2
dc.institutionauthor Akten, Ebru Demet en_US
dc.language.iso en en_US
dc.publisher Springer en_US
dc.relation.journal Journal of Computer-Aided Molecular Design en_US
dc.relation.publicationcategory Makale - Uluslararası Hakemli Dergi - Kurum Öğretim Elemanı en_US
dc.rights info:eu-repo/semantics/openAccess en_US
dc.scopus.citedbyCount 1
dc.subject PDE4B en_US
dc.subject IC50 en_US
dc.subject Molecular docking en_US
dc.subject Molecular dynamics en_US
dc.subject MM-GB/SA en_US
dc.title Assessing Protein-Ligand Binding Modes With Computational Tools: the Case of Pde4b en_US
dc.type Article en_US
dc.wos.citedbyCount 1
dspace.entity.type Publication
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relation.isOrgUnitOfPublication 71ce8622-7449-4a6a-8fad-44d881416546
relation.isOrgUnitOfPublication.latestForDiscovery 71ce8622-7449-4a6a-8fad-44d881416546

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