dc.contributor.author | Ivani, Ivan |
dc.contributor.author | Dans, Pablo D. |
dc.contributor.author | Noy, Agnes |
dc.contributor.author | Pérez, Alberto |
dc.contributor.author | Faustino, Ignacio |
dc.contributor.author | Hospital, Adam |
dc.contributor.author | Walther, Jürgen |
dc.contributor.author | Andrio, Pau |
dc.contributor.author | Goñi, Ramon |
dc.contributor.author | Balanceanu, Alexandra |
dc.contributor.author | Portella, Guillem |
dc.contributor.author | Battistini, Federica |
dc.contributor.author | Gelpí, Josep Lluís |
dc.contributor.author | González, Carlos |
dc.contributor.author | Vendruscolo, Michele |
dc.contributor.author | Laughton, Charles A. |
dc.contributor.author | Harris, Sarah A. |
dc.contributor.author | Case, David A. |
dc.contributor.author | Orozco, Modesto |
dc.contributor.other | Barcelona Supercomputing Center |
dc.date.accessioned | 2016-03-14T15:54:26Z |
dc.date.available | 2016-05-17T00:30:32Z |
dc.date.issued | 2015-11-16 |
dc.identifier.citation | Ivani, Ivan [et al.]. PARMBSC1: A refined force-field for DNA simulations. "Nature Methods", 16 Novembre 2015, vol. 13, p. 55-58. |
dc.identifier.issn | 1548-7091 |
dc.identifier.uri | http://hdl.handle.net/2117/84332 |
dc.description.abstract | 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/. |
dc.description.sponsorship | 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. |
dc.format.extent | 4 p. |
dc.language.iso | eng |
dc.publisher | Nature Publishing Group |
dc.subject | Àrees temàtiques de la UPC::Enginyeria mecànica |
dc.subject.lcsh | DNA--Analysis |
dc.subject.lcsh | Simulation methods |
dc.subject.other | Computational biophysics |
dc.subject.other | Computational models |
dc.subject.other | DNA |
dc.title | PARMBSC1: A refined force-field for DNA simulations |
dc.type | Article |
dc.subject.lemac | ADN |
dc.subject.lemac | Simulació, Mètodes de |
dc.identifier.doi | 10.1038/nmeth.3658 |
dc.description.peerreviewed | Peer Reviewed |
dc.relation.publisherversion | http://www.nature.com/nmeth/journal/v13/n1/full/nmeth.3658.html |
dc.rights.access | Open Access |
dc.description.version | Postprint (author's final draft) |
dc.relation.projectid | info: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.projectid | info:eu-repo/grantAgreement/EC/FP7/291433/EU/Advanced multiscale simulation of DNA/SIMDNA |
dc.relation.projectid | info:eu-repo/grantAgreement/EC/H2020/675728/EU/Centre of Excellence for Biomolecular Research/BioExcel |
dc.relation.projectid | info: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.publicationName | Nature Methods |
local.citation.volume | 13 |
local.citation.startingPage | 55 |
local.citation.endingPage | 58 |
dc.identifier.pmid | 26569599 |