PARMBSC1: A refined force-field for DNA simulations

Ivani, Ivan; Dans, Pablo D.; Noy, Agnes; Pérez, Alberto; Faustino, Ignacio; Hospital, Adam; Walther, Jürgen; Andrio, Pau; Goñi, Ramon; Balanceanu, Alexandra; Portella, Guillem; Battistini, Federica; Gelpí, Josep Lluís; González, Carlos; Vendruscolo, Michele; Laughton, Charles A.; Harris, Sarah A.; Case, David A.; Orozco, Modesto

PARMBSC1: A refined force-field for DNA simulations

We 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 d...

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Authors:	Ivani, Ivan, Dans, Pablo D., Noy, Agnes, Pérez, Alberto, Faustino, Ignacio, Hospital, Adam, Walther, Jürgen, Andrio, Pau, Goñi, Ramon, Balanceanu, Alexandra, Portella, Guillem, Battistini, Federica, Gelpí, Josep Lluís, González, Carlos, Vendruscolo, Michele, Laughton, Charles A., Harris, Sarah A., Case, David A., Orozco, Modesto
Format:	article
Publication Date:	2015
Country:	España
Institution:	Universitat Politècnica de Catalunya (UPC)
Repository:	UPCommons. Portal del coneixement obert de la UPC
Language:	English
OAI Identifier:	oai:upcommons.upc.edu:2117/84332
Online Access:	https://hdl.handle.net/2117/84332 https://dx.doi.org/10.1038/nmeth.3658
Access Level:	Open access
Keyword:	DNA--Analysis Simulation methods Computational biophysics Computational models DNA ADN Simulació, Mètodes de Àrees temàtiques de la UPC::Enginyeria mecànica

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spelling	PARMBSC1: A refined force-field for DNA simulationsIvani, IvanDans, Pablo D.Noy, AgnesPérez, AlbertoFaustino, IgnacioHospital, AdamWalther, JürgenAndrio, PauGoñi, RamonBalanceanu, AlexandraPortella, GuillemBattistini, FedericaGelpí, Josep LluísGonzález, CarlosVendruscolo, MicheleLaughton, Charles A.Harris, Sarah A.Case, David A.Orozco, ModestoDNA--AnalysisSimulation methodsComputational biophysicsComputational modelsDNAADNSimulació, Mètodes deÀrees temàtiques de la UPC::Enginyeria mecànicaWe 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/.MO 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.Peer ReviewedNature Publishing Group20152015-11-1620162016-03-14journal articlehttp://purl.org/coar/resource_type/c_6501AMhttp://purl.org/coar/version/c_ab4af688f83e57aainfo:eu-repo/semantics/articleapplication/pdfhttps://hdl.handle.net/2117/84332https://dx.doi.org/10.1038/nmeth.365826569599reponame:UPCommons. Portal del coneixement obert de la UPCinstname:Universitat Politècnica de Catalunya (UPC)InglésengMinisterio de Economía y Competitividad http://doi.org/10.13039/501100003329 BIO2012-32868 ESTUDIO DE FORMAS INUSUALES O TENSIONADAS DE LOS ACIDOS NUCLEICOS DE POTENCIAL INTERES BIOMEDICO O BIOTECNOLOGICOEuropean Commission http://dx.doi.org/10.13039/100011102 Seventh Framework Programme 291433 Advanced multiscale simulation of DNAEuropean Commission http://doi.org/10.13039/100010661 Horizon 2020 Framework Programme 675728 Centre of Excellence for Biomolecular ResearchEuropean Commission http://doi.org/10.13039/100010661 Horizon 2020 Framework Programme 654812 Development of a multiscale modeling strategy to decipher how hybrid DNA%2FRNA triplexes and G-quadruplexes affect gene expression regulationopen accesshttp://purl.org/coar/access_right/c_abf2info:eu-repo/semantics/openAccessoai:upcommons.upc.edu:2117/843322026-05-27T15:37:01Z
dc.title.none.fl_str_mv	PARMBSC1: A refined force-field for DNA simulations
title	PARMBSC1: A refined force-field for DNA simulations
spellingShingle	PARMBSC1: A refined force-field for DNA simulations Ivani, Ivan DNA--Analysis Simulation methods Computational biophysics Computational models DNA ADN Simulació, Mètodes de Àrees temàtiques de la UPC::Enginyeria mecànica
title_short	PARMBSC1: A refined force-field for DNA simulations
title_full	PARMBSC1: A refined force-field for DNA simulations
title_fullStr	PARMBSC1: A refined force-field for DNA simulations
title_full_unstemmed	PARMBSC1: A refined force-field for DNA simulations
title_sort	PARMBSC1: A refined force-field for DNA simulations
dc.creator.none.fl_str_mv	Ivani, Ivan Dans, Pablo D. Noy, Agnes Pérez, Alberto Faustino, Ignacio Hospital, Adam Walther, Jürgen Andrio, Pau Goñi, Ramon Balanceanu, Alexandra Portella, Guillem Battistini, Federica Gelpí, Josep Lluís González, Carlos Vendruscolo, Michele Laughton, Charles A. Harris, Sarah A. Case, David A. Orozco, Modesto
author	Ivani, Ivan
author_facet	Ivani, Ivan Dans, Pablo D. Noy, Agnes Pérez, Alberto Faustino, Ignacio Hospital, Adam Walther, Jürgen Andrio, Pau Goñi, Ramon Balanceanu, Alexandra Portella, Guillem Battistini, Federica Gelpí, Josep Lluís González, Carlos Vendruscolo, Michele Laughton, Charles A. Harris, Sarah A. Case, David A. Orozco, Modesto
author_role	author
author2	Dans, Pablo D. Noy, Agnes Pérez, Alberto Faustino, Ignacio Hospital, Adam Walther, Jürgen Andrio, Pau Goñi, Ramon Balanceanu, Alexandra Portella, Guillem Battistini, Federica Gelpí, Josep Lluís González, Carlos Vendruscolo, Michele Laughton, Charles A. Harris, Sarah A. Case, David A. Orozco, Modesto
author2_role	author author author author author author author author author author author author author author author author author author
dc.subject.none.fl_str_mv	DNA--Analysis Simulation methods Computational biophysics Computational models DNA ADN Simulació, Mètodes de Àrees temàtiques de la UPC::Enginyeria mecànica
topic	DNA--Analysis Simulation methods Computational biophysics Computational models DNA ADN Simulació, Mètodes de Àrees temàtiques de la UPC::Enginyeria mecànica
description	We 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/.
publishDate	2015
dc.date.none.fl_str_mv	2015 2015-11-16 2016 2016-03-14
dc.type.none.fl_str_mv	journal article http://purl.org/coar/resource_type/c_6501 AM http://purl.org/coar/version/c_ab4af688f83e57aa
dc.type.openaire.fl_str_mv	info:eu-repo/semantics/article
format	article
dc.identifier.none.fl_str_mv	https://hdl.handle.net/2117/84332 https://dx.doi.org/10.1038/nmeth.3658 26569599
url	https://hdl.handle.net/2117/84332 https://dx.doi.org/10.1038/nmeth.3658
identifier_str_mv	26569599
dc.language.none.fl_str_mv	Inglés eng
language_invalid_str_mv	Inglés
language	eng
dc.relation.none.fl_str_mv	Ministerio de Economía y Competitividad http://doi.org/10.13039/501100003329 BIO2012-32868 ESTUDIO DE FORMAS INUSUALES O TENSIONADAS DE LOS ACIDOS NUCLEICOS DE POTENCIAL INTERES BIOMEDICO O BIOTECNOLOGICO European Commission http://dx.doi.org/10.13039/100011102 Seventh Framework Programme 291433 Advanced multiscale simulation of DNA European Commission http://doi.org/10.13039/100010661 Horizon 2020 Framework Programme 675728 Centre of Excellence for Biomolecular Research European Commission http://doi.org/10.13039/100010661 Horizon 2020 Framework Programme 654812 Development of a multiscale modeling strategy to decipher how hybrid DNA%2FRNA triplexes and G-quadruplexes affect gene expression regulation
dc.rights.none.fl_str_mv	open access http://purl.org/coar/access_right/c_abf2
dc.rights.openaire.fl_str_mv	info:eu-repo/semantics/openAccess
rights_invalid_str_mv	open access http://purl.org/coar/access_right/c_abf2
eu_rights_str_mv	openAccess
dc.format.none.fl_str_mv	application/pdf
dc.publisher.none.fl_str_mv	Nature Publishing Group
publisher.none.fl_str_mv	Nature Publishing Group
dc.source.none.fl_str_mv	reponame:UPCommons. Portal del coneixement obert de la UPC instname:Universitat Politècnica de Catalunya (UPC)
instname_str	Universitat Politècnica de Catalunya (UPC)
reponame_str	UPCommons. Portal del coneixement obert de la UPC
collection	UPCommons. Portal del coneixement obert de la UPC
repository.name.fl_str_mv
repository.mail.fl_str_mv
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PARMBSC1: A refined force-field for DNA simulations

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