The ABCs of molecular dynamics simulations on B-DNA, circa 2012

David L. Beveridge, Thomas E. Cheatham, Mihaly Mezei

Research output: Contribution to journalArticlepeer-review

52 Scopus citations

Abstract

This article provides a retrospective on the ABC initiative in the area of all-atom molecular dynamics (MD) simulations including explicit solvent on all tetranucleotide steps of duplex B-form DNA duplex, ca. 2012. The ABC consortium has completed two phases of simulations, the most current being a set of 50-100 trajectories based on the AMBER ff99 force field together with the parmbsc0 modification. Some general perspectives on the field of MD on DNA and sequence effects on DNA structure are provided, followed by an overview our MD results, including a detailed comparison of the ff99/parmbsc0 results with crystal and NMR structures available for d(CGCGAATTCGCG). Some projects inspired by or related to the ABC initiative and database are also reviewed, including methods for the trajectory analyses, informatics of dealing with the large database of results, compressions of trajectories for efficacy of distribution, DNA solvation by water and ions, parameterization of coarse-grained models with applications and gene finding and genome annotation.

Original languageEnglish
Pages (from-to)379-397
Number of pages19
JournalJournal of Biosciences
Volume37
Issue number3
DOIs
StatePublished - Jul 2012

Keywords

  • ABC
  • DNA
  • Molecular dynamics
  • Sequence effects
  • Tetranucleotide steps

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