TUPÃ: Electric field analyses for molecular simulations

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dc.contributor.authorPolêto, Marcelo D.en
dc.contributor.authorLemkul, Justin A.en
dc.date.accessioned2023-01-12T19:20:22Zen
dc.date.available2023-01-12T19:20:22Zen
dc.date.issued2022-04-22en
dc.date.updated2023-01-12T18:41:47Zen
dc.description.abstractWe introduce TUPÃ, a Python-based algorithm to calculate and analyze electric fields in molecular simulations. To demonstrate the features in TUPÃ, we present three test cases in which the orientation and magnitude of the electric field exerted by biomolecules help explain biological phenomena or observed kinetics. As part of TUPÃ, we also provide a PyMOL plugin to help researchers visualize how electric fields are organized within the simulation system. The code is freely available and can be obtained at https://mdpoleto.github.io/tupa/.en
dc.description.versionAccepted versionen
dc.format.extentPages 1113-1119en
dc.format.extent7 page(s)en
dc.format.mimetypeapplication/pdfen
dc.identifier.doihttps://doi.org/10.1002/jcc.26873en
dc.identifier.eissn1096-987Xen
dc.identifier.issn0192-8651en
dc.identifier.issue16en
dc.identifier.orcidLemkul, Justin [0000-0001-6661-8653]en
dc.identifier.pmid35460102en
dc.identifier.urihttp://hdl.handle.net/10919/113151en
dc.identifier.volume43en
dc.language.isoenen
dc.publisherWileyen
dc.relation.urihttp://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcApp=PARTNER_APP&SrcAuth=LinksAMR&KeyUT=WOS:000785574800001&DestLinkType=FullRecord&DestApp=ALL_WOS&UsrCustomerID=930d57c9ac61a043676db62af60056c1en
dc.rightsCreative Commons Attribution-NonCommercial-NoDerivatives 4.0 Internationalen
dc.rights.urihttp://creativecommons.org/licenses/by-nc-nd/4.0/en
dc.subjectelectric fielden
dc.subjectelectrostaticsen
dc.subjectforce fieldsen
dc.subjectmolecular dynamicsen
dc.subjectmolecular mechanicsen
dc.subjectPARTICLE MESH EWALDen
dc.subjectDYNAMICS SIMULATIONSen
dc.subjectELECTROSTATIC FIELDSen
dc.subjectCATALYSISen
dc.subjectSITESen
dc.subjectPOWERen
dc.subjectBioengineeringen
dc.subject.meshElectricityen
dc.subject.meshKineticsen
dc.subject.meshMolecular Dynamics Simulationen
dc.titleTUPÃ: Electric field analyses for molecular simulationsen
dc.title.serialJournal of Computational Chemistryen
dc.typeArticle - Refereeden
dc.type.dcmitypeTexten
dc.type.otherArticleen
dc.type.otherJournalen
dcterms.dateAccepted2022-04-08en
pubs.organisational-group/Virginia Techen
pubs.organisational-group/Virginia Tech/Agriculture & Life Sciencesen
pubs.organisational-group/Virginia Tech/Agriculture & Life Sciences/Biochemistryen
pubs.organisational-group/Virginia Tech/All T&R Facultyen
pubs.organisational-group/Virginia Tech/Agriculture & Life Sciences/CALS T&R Facultyen

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