Journal
NUCLEIC ACIDS RESEARCH
Volume 48, Issue 5, Pages -Publisher
OXFORD UNIV PRESS
DOI: 10.1093/nar/gkaa015
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Funding
- Spanish Ministry of Science [BFU2014-61670-EXP, BFU2014-52864-R]
- Catalan SGR, the Instituto Nacional de Bioinformatica
- European Research Council (ERC SimDNA), European Union's Horizon 2020 Research and Innovation Program [676556]
- Biomolecular and Bioinformatics Resources Platform - Fondo Europeo de Desarrollo Regional (FEDER) [ISCIII PT 13/0001/0030]
- MINECO Severo Ochoa Award of Excellence (Government of Spain)
- PEDECIBA (Programa de Desarrollo de las Ciencias Basicas)
- SNI (Sistema Nacional de Investigadores, Agencia Nacional de Investigacion e Innovacion, Uruguay)
- ICREA (Institucio Catalana de Recerca i Estudis Avancats)
- European Union's Horizon 2020 Research and Innovation Program [676556]
- La Caixa PhD Fellowship (UB, Spain)
- La Caixa PhD Fellowship (IRB Barcelona, Spain)
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We present a new coarse grained method for the simulation of duplex DNA. The algorithm uses a generalized multi-harmonic model that can represent any multi-normal distribution of helical parameters, thus avoiding caveats of current mesoscopic models for DNA simulation and representing a breakthrough in the field. The method has been parameterized from accurate parmbscl atomistic molecular dynamics simulations of all unique tetranucleotide sequences of DNA embedded in long duplexes and takes advantage of the correlation between helical states and backbone configurations to derive atomistic representations of DNA. The algorithm, which is implemented in a simple web interface and in a standalone package reproduces with high computational efficiency the structural landscape of long segments of DNA untreatable by atomistic molecular dynamics simulations.
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