000866016 001__ 866016
000866016 005__ 20240625095119.0
000866016 0247_ $$2doi$$a10.1021/acs.jpclett.9b01183
000866016 0247_ $$2Handle$$a2128/23195
000866016 0247_ $$2altmetric$$aaltmetric:62021665
000866016 0247_ $$2pmid$$apmid:31188006
000866016 0247_ $$2WOS$$aWOS:000472804700048
000866016 037__ $$aFZJ-2019-05276
000866016 082__ $$a530
000866016 1001_ $$0P:(DE-Juel1)174546$$aCapelli, Riccardo$$b0$$eCorresponding author
000866016 245__ $$aExhaustive Search of Ligand Binding Pathways via Volume-Based Metadynamics
000866016 260__ $$aWashington, DC$$bACS$$c2019
000866016 3367_ $$2DRIVER$$aarticle
000866016 3367_ $$2DataCite$$aOutput Types/Journal article
000866016 3367_ $$0PUB:(DE-HGF)16$$2PUB:(DE-HGF)$$aJournal Article$$bjournal$$mjournal$$s1674540522_23238
000866016 3367_ $$2BibTeX$$aARTICLE
000866016 3367_ $$2ORCID$$aJOURNAL_ARTICLE
000866016 3367_ $$00$$2EndNote$$aJournal Article
000866016 520__ $$aDetermining the complete set of ligands’ binding–unbinding pathways is important for drug discovery and for rational interpretation of mutation data. Here we have developed a metadynamics-based technique that addresses this issue and allows estimating affinities in the presence of multiple escape pathways. Our approach is shown on a lysozyme T4 variant in complex with a benzene molecule. The calculated binding free energy is in agreement with experimental data. Remarkably, not only were we able to find all the previously identified ligand binding pathways, but also we identified three pathways previously not identified as such. These results were obtained at a small computational cost, making this approach valuable for practical applications, such as screening of small compound libraries.
000866016 536__ $$0G:(DE-HGF)POF3-574$$a574 - Theory, modelling and simulation (POF3-574)$$cPOF3-574$$fPOF III$$x0
000866016 536__ $$0G:(EU-Grant)785907$$aHBP SGA2 - Human Brain Project Specific Grant Agreement 2 (785907)$$c785907$$fH2020-SGA-FETFLAG-HBP-2017$$x1
000866016 536__ $$0G:(DE-Juel1)jias5d_20181101$$aHPC-aided design of drugs with improved kinetics of binding (jias5d_20181101)$$cjias5d_20181101$$fHPC-aided design of drugs with improved kinetics of binding$$x2
000866016 588__ $$aDataset connected to CrossRef
000866016 7001_ $$0P:(DE-Juel1)145614$$aCarloni, Paolo$$b1
000866016 7001_ $$0P:(DE-HGF)0$$aParrinello, Michele$$b2
000866016 773__ $$0PERI:(DE-600)2522838-9$$a10.1021/acs.jpclett.9b01183$$gVol. 10, no. 12, p. 3495 - 3499$$n12$$p3495 - 3499$$tThe journal of physical chemistry letters$$v10$$x1948-7185$$y2019
000866016 8564_ $$uhttps://juser.fz-juelich.de/record/866016/files/1904.10726.pdf$$yPublished on 2019-06-03. Available in OpenAccess from 2020-06-03.
000866016 8564_ $$uhttps://juser.fz-juelich.de/record/866016/files/Sphere.pdf$$yPublished on 2019-06-03. Available in OpenAccess from 2020-06-03.
000866016 8564_ $$uhttps://juser.fz-juelich.de/record/866016/files/acs.jpclett.9b01183.pdf$$yRestricted
000866016 8564_ $$uhttps://juser.fz-juelich.de/record/866016/files/1904.10726.pdf?subformat=pdfa$$xpdfa$$yPublished on 2019-06-03. Available in OpenAccess from 2020-06-03.
000866016 8564_ $$uhttps://juser.fz-juelich.de/record/866016/files/Sphere.pdf?subformat=pdfa$$xpdfa$$yPublished on 2019-06-03. Available in OpenAccess from 2020-06-03.
000866016 8564_ $$uhttps://juser.fz-juelich.de/record/866016/files/acs.jpclett.9b01183.pdf?subformat=pdfa$$xpdfa$$yRestricted
000866016 909CO $$ooai:juser.fz-juelich.de:866016$$pdnbdelivery$$pec_fundedresources$$pVDB$$pdriver$$popen_access$$popenaire
000866016 9101_ $$0I:(DE-588b)5008462-8$$6P:(DE-Juel1)174546$$aForschungszentrum Jülich$$b0$$kFZJ
000866016 9101_ $$0I:(DE-588b)5008462-8$$6P:(DE-Juel1)145614$$aForschungszentrum Jülich$$b1$$kFZJ
000866016 9131_ $$0G:(DE-HGF)POF3-574$$1G:(DE-HGF)POF3-570$$2G:(DE-HGF)POF3-500$$3G:(DE-HGF)POF3$$4G:(DE-HGF)POF$$aDE-HGF$$bKey Technologies$$lDecoding the Human Brain$$vTheory, modelling and simulation$$x0
000866016 9141_ $$y2019
000866016 915__ $$0StatID:(DE-HGF)0200$$2StatID$$aDBCoverage$$bSCOPUS
000866016 915__ $$0StatID:(DE-HGF)0530$$2StatID$$aEmbargoed OpenAccess
000866016 915__ $$0StatID:(DE-HGF)0100$$2StatID$$aJCR$$bJ PHYS CHEM LETT : 2017
000866016 915__ $$0StatID:(DE-HGF)9905$$2StatID$$aIF >= 5$$bJ PHYS CHEM LETT : 2017
000866016 915__ $$0StatID:(DE-HGF)0150$$2StatID$$aDBCoverage$$bWeb of Science Core Collection
000866016 915__ $$0StatID:(DE-HGF)0110$$2StatID$$aWoS$$bScience Citation Index
000866016 915__ $$0StatID:(DE-HGF)0111$$2StatID$$aWoS$$bScience Citation Index Expanded
000866016 915__ $$0StatID:(DE-HGF)1150$$2StatID$$aDBCoverage$$bCurrent Contents - Physical, Chemical and Earth Sciences
000866016 915__ $$0StatID:(DE-HGF)0310$$2StatID$$aDBCoverage$$bNCBI Molecular Biology Database
000866016 915__ $$0StatID:(DE-HGF)0300$$2StatID$$aDBCoverage$$bMedline
000866016 915__ $$0StatID:(DE-HGF)0199$$2StatID$$aDBCoverage$$bClarivate Analytics Master Journal List
000866016 920__ $$lyes
000866016 9201_ $$0I:(DE-Juel1)IAS-5-20120330$$kIAS-5$$lComputational Biomedicine$$x0
000866016 9201_ $$0I:(DE-82)080012_20140620$$kJARA-HPC$$lJARA - HPC$$x1
000866016 9201_ $$0I:(DE-Juel1)INM-9-20140121$$kINM-9$$lComputational Biomedicine$$x2
000866016 980__ $$ajournal
000866016 980__ $$aVDB
000866016 980__ $$aI:(DE-Juel1)IAS-5-20120330
000866016 980__ $$aI:(DE-82)080012_20140620
000866016 980__ $$aI:(DE-Juel1)INM-9-20140121
000866016 980__ $$aUNRESTRICTED
000866016 9801_ $$aFullTexts