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.
journal_name
Nucleic Acids Resjournal_title
Nucleic acids researchauthors
Walther J,Dans PD,Balaceanu A,Hospital A,Bayarri G,Orozco Mdoi
10.1093/nar/gkaa015subject
Has Abstractpub_date
2020-03-18 00:00:00pages
e29issue
5eissn
0305-1048issn
1362-4962pii
5709710journal_volume
48pub_type
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