A multi-modal coarse grained model of DNA flexibility mappable to the atomistic level

TitleA multi-modal coarse grained model of DNA flexibility mappable to the atomistic level
Publication TypeJournal Article
Year of Publication2020
AuthorsWalther, Jurgen, Dans Pablo D., Balaceanu Alexandra, Hospital Adam, Bayarri Genis, and Orozco Modesto
JournalNucleic Acids Research
Date Published01/2020
ISBN Number0305-1048
Abstract

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 parmbsc1 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.

URLhttps://doi.org/10.1093/nar/gkaa015
Short TitleNucleic Acids Research
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