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Article: Hepatitis C virus NS5B polymerase: QM/MM calculations show the important role of the internal energy in ligand binding

TitleHepatitis C virus NS5B polymerase: QM/MM calculations show the important role of the internal energy in ligand binding
Authors
Issue Date2008
PublisherAmerican Chemical Society. The Journal's web site is located at http://pubs.acs.org/journal/jpcbfk
Citation
Journal Of Physical Chemistry B, 2008, v. 112 n. 10, p. 3168-3176 How to Cite?
AbstractThe inter- and intramolecular interactions that determine the experimentally observed binding mode of the ligand (2Z)-2-(benzoylamino)-3-[4- (2-bromophenoxy)phenyl]-2-propenoate in complex with hepatitis C virus NS5B polymerase have been studied using QM/MM calculations. DFT-based QM/MM optimizations were performed on a number of ligand conformers in the protein-ligand complex. Using these initial poses, our aim is 2-fold. First, we identify the minimum energy pose. Second, we dissect the energetic contributions to this pose using QM/MM methods. The study reveals the critical importance of internal energy for the proper energy ranking of the docked poses. Using this protocol, we successfully identified three poses that have low RMSD with respect to the crystallographic structure from among the top 20 initially docked poses. We show that the most important energetic component contributing to binding for this particular protein-ligand system is the conformational (i.e., QM internal) energy. © 2008 American Chemical Society.
Persistent Identifierhttp://hdl.handle.net/10722/168295
ISSN
2015 Impact Factor: 3.187
2015 SCImago Journal Rankings: 1.414
ISI Accession Number ID
References

 

DC FieldValueLanguage
dc.contributor.authorParks, JMen_US
dc.contributor.authorKondru, RKen_US
dc.contributor.authorHu, Hen_US
dc.contributor.authorBeratan, DNen_US
dc.contributor.authorYang, Wen_US
dc.date.accessioned2012-10-08T03:17:10Z-
dc.date.available2012-10-08T03:17:10Z-
dc.date.issued2008en_US
dc.identifier.citationJournal Of Physical Chemistry B, 2008, v. 112 n. 10, p. 3168-3176en_US
dc.identifier.issn1520-6106en_US
dc.identifier.urihttp://hdl.handle.net/10722/168295-
dc.description.abstractThe inter- and intramolecular interactions that determine the experimentally observed binding mode of the ligand (2Z)-2-(benzoylamino)-3-[4- (2-bromophenoxy)phenyl]-2-propenoate in complex with hepatitis C virus NS5B polymerase have been studied using QM/MM calculations. DFT-based QM/MM optimizations were performed on a number of ligand conformers in the protein-ligand complex. Using these initial poses, our aim is 2-fold. First, we identify the minimum energy pose. Second, we dissect the energetic contributions to this pose using QM/MM methods. The study reveals the critical importance of internal energy for the proper energy ranking of the docked poses. Using this protocol, we successfully identified three poses that have low RMSD with respect to the crystallographic structure from among the top 20 initially docked poses. We show that the most important energetic component contributing to binding for this particular protein-ligand system is the conformational (i.e., QM internal) energy. © 2008 American Chemical Society.en_US
dc.languageengen_US
dc.publisherAmerican Chemical Society. The Journal's web site is located at http://pubs.acs.org/journal/jpcbfken_US
dc.relation.ispartofJournal of Physical Chemistry Ben_US
dc.titleHepatitis C virus NS5B polymerase: QM/MM calculations show the important role of the internal energy in ligand bindingen_US
dc.typeArticleen_US
dc.identifier.emailHu, H:haohu@hku.hken_US
dc.identifier.authorityHu, H=rp00707en_US
dc.description.naturelink_to_subscribed_fulltexten_US
dc.identifier.doi10.1021/jp076885jen_US
dc.identifier.pmid18271573-
dc.identifier.scopuseid_2-s2.0-42449130535en_US
dc.relation.referenceshttp://www.scopus.com/mlt/select.url?eid=2-s2.0-42449130535&selection=ref&src=s&origin=recordpageen_US
dc.identifier.volume112en_US
dc.identifier.issue10en_US
dc.identifier.spage3168en_US
dc.identifier.epage3176en_US
dc.identifier.isiWOS:000253784700054-
dc.publisher.placeUnited Statesen_US
dc.identifier.scopusauthoridParks, JM=10143634800en_US
dc.identifier.scopusauthoridKondru, RK=6603189176en_US
dc.identifier.scopusauthoridHu, H=7404097564en_US
dc.identifier.scopusauthoridBeratan, DN=7006677556en_US
dc.identifier.scopusauthoridYang, W=35265650900en_US
dc.identifier.citeulike2373313-

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