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PARMBSC1: A refined force-field for DNA simulations

dc.contributor.authorIvani, Ivan
dc.contributor.authorDans, Pablo D.
dc.contributor.authorNoy, Agnes
dc.contributor.authorPérez, Alberto
dc.contributor.authorFaustino, Ignacio
dc.contributor.authorHospital, Adam
dc.contributor.authorWalther, Jürgen
dc.contributor.authorAndrio, Pau
dc.contributor.authorGoñi, Ramon
dc.contributor.authorBalanceanu, Alexandra
dc.contributor.authorPortella, Guillem
dc.contributor.authorBattistini, Federica
dc.contributor.authorGelpí, Josep Lluís
dc.contributor.authorGonzález, Carlos
dc.contributor.authorVendruscolo, Michele
dc.contributor.authorLaughton, Charles A.
dc.contributor.authorHarris, Sarah A.
dc.contributor.authorCase, David A.
dc.contributor.authorOrozco, Modesto
dc.contributor.otherBarcelona Supercomputing Center
dc.date.accessioned2016-03-14T15:54:26Z
dc.date.available2016-05-17T00:30:32Z
dc.date.issued2015-11-16
dc.identifier.citationIvani, Ivan [et al.]. PARMBSC1: A refined force-field for DNA simulations. "Nature Methods", 16 Novembre 2015, vol. 13, p. 55-58.
dc.identifier.issn1548-7091
dc.identifier.urihttp://hdl.handle.net/2117/84332
dc.description.abstractWe present parmbsc1, a force field for DNA atomistic simulation, which has been parameterized from high-level quantum mechanical data and tested for nearly 100 systems (representing a total simulation time of ~140 μs) covering most of DNA structural space. Parmbsc1 provides high-quality results in diverse systems. Parameters and trajectories are available at http://mmb.irbbarcelona.org/ParmBSC1/.
dc.description.sponsorshipMO thanks Spanish Ministry of Science (BIO2012-32868), the Catalan SGR, the Instituto Nacional de Bioinformática, and the European Research Council (ERC_SimDNA) for support. MO is an ICREA academia researcher. MO thanks CPU/GPU time on MareNostrum/MinoTauro (BSC). CAL, SAH and AN thanks the UK HECBioSim Consortium for HPC time on ARCHER (Grant EP/L000253/1). AN was supported by the Biotechnology and Biological Sciences Research Council (BBSRC, grant number BB/I019294/1), and thanks ARC Leeds for computational resources. PDD is a PEDECIBA and SNI (ANII, Uruguay) researcher. DAC thanks Chunmei Liu for assistance with the crystal simulation analysis.
dc.format.extent4 p.
dc.language.isoeng
dc.publisherNature Publishing Group
dc.subjectÀrees temàtiques de la UPC::Enginyeria mecànica
dc.subject.lcshDNA--Analysis
dc.subject.lcshSimulation methods
dc.subject.otherComputational biophysics
dc.subject.otherComputational models
dc.subject.otherDNA
dc.titlePARMBSC1: A refined force-field for DNA simulations
dc.typeArticle
dc.subject.lemacADN
dc.subject.lemacSimulació, Mètodes de
dc.identifier.doi10.1038/nmeth.3658
dc.description.peerreviewedPeer Reviewed
dc.relation.publisherversionhttp://www.nature.com/nmeth/journal/v13/n1/full/nmeth.3658.html
dc.rights.accessOpen Access
dc.description.versionPostprint (author's final draft)
dc.relation.projectidinfo:eu-repo/grantAgreement/MINECO//BIO2012-32868/ES/ESTUDIO DE FORMAS INUSUALES O TENSIONADAS DE LOS ACIDOS NUCLEICOS DE POTENCIAL INTERES BIOMEDICO O BIOTECNOLOGICO/
dc.relation.projectidinfo:eu-repo/grantAgreement/EC/FP7/291433/EU/Advanced multiscale simulation of DNA/SIMDNA
dc.relation.projectidinfo:eu-repo/grantAgreement/EC/H2020/675728/EU/Centre of Excellence for Biomolecular Research/BioExcel
dc.relation.projectidinfo:eu-repo/grantAgreement/EC/H2020/654812/EU/Development of a multiscale modeling strategy to decipher how hybrid DNA%2FRNA triplexes and G-quadruplexes affect gene expression regulation/HoogsCG
local.citation.publicationNameNature Methods
local.citation.volume13
local.citation.startingPage55
local.citation.endingPage58
dc.identifier.pmid26569599


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