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PARMBSC1: A refined force-field for DNA simulations

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10.1038/nmeth.3658
 
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hdl:2117/84332

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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
Document typeArticle
Defense date2015-11-16
PublisherNature Publishing Group
Rights accessOpen Access
All rights reserved. This work is protected by the corresponding intellectual and industrial property rights. Without prejudice to any existing legal exemptions, reproduction, distribution, public communication or transformation of this work are prohibited without permission of the copyright holder
ProjectESTUDIO DE FORMAS INUSUALES O TENSIONADAS DE LOS ACIDOS NUCLEICOS DE POTENCIAL INTERES BIOMEDICO O BIOTECNOLOGICO (MINECO-BIO2012-32868)
SIMDNA - Advanced multiscale simulation of DNA (EC-FP7-291433)
BioExcel - Centre of Excellence for Biomolecular Research (EC-H2020-675728)
HoogsCG - Development of a multiscale modeling strategy to decipher how hybrid DNA%2FRNA triplexes and G-quadruplexes affect gene expression regulation (EC-H2020-654812)
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/.
CitationIvani, Ivan [et al.]. PARMBSC1: A refined force-field for DNA simulations. "Nature Methods", 16 Novembre 2015, vol. 13, p. 55-58. 
URIhttp://hdl.handle.net/2117/84332
DOI10.1038/nmeth.3658
ISSN1548-7091
Publisher versionhttp://www.nature.com/nmeth/journal/v13/n1/full/nmeth.3658.html
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