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research article

Towards a molecular dynamics consensus view of B-DNA flexibility

Perez, Alberto
•
Lankas, Filip
•
Luque, F. Javier
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2008
Nucleic Acids Research

We present a systematic study of B-DNA flexibility in aqueous solution using long-scale molecular dynamics simulations with the two more recent versions of nucleic acids force fields (CHARMM27 and parmbsc0) using four long duplexes designed to contain several copies of each individual base pair step. Our study highlights some differences between pambsc0 and CHARMM27 families of simulations, but also extensive agreement in the representation of DNA flexibility. We also performed additional simulations with the older AMBER force fields parm94 and parm99, corrected for non-canonical backbone flips. Taken together, the results allow us to draw for the first time a consensus molecular dynamics picture of B-DNA flexibility.

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Type
research article
DOI
10.1093/nar/gkn082
Web of Science ID

WOS:000255152200032

Author(s)
Perez, Alberto
Lankas, Filip
Luque, F. Javier
Orozco, Modesto
Date Issued

2008

Publisher

Oxford University Press

Published in
Nucleic Acids Research
Volume

36

Start page

2379

End page

2394

Subjects

Unique Tetranucleotide Sequences

•

Transcription Start Sites

•

Empirical Force-Field

•

Particle Mesh Ewald

•

Nucleic-Acids

•

Escherichia-Coli

•

Excision-Repair

•

Human Genome

•

Simulations

•

Rna

Note

National Licences

Editorial or Peer reviewed

REVIEWED

Written at

EPFL

EPFL units
LCVMM  
Available on Infoscience
November 30, 2010
Use this identifier to reference this record
https://infoscience.epfl.ch/handle/20.500.14299/61458
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