Format

Send to

Choose Destination
See comment in PubMed Commons below
J Biosci. 2012 Jul;37(3):379-97.

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

Author information

  • 1Department of Chemistry and Molecular Biophysics Program, Wesleyan University Middletown, CT 06459, USA. dbeveridge@wesleyan.edu

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.

PMID:
22750978
PMCID:
PMC4029509
[PubMed - indexed for MEDLINE]
Free PMC Article
PubMed Commons home

PubMed Commons

0 comments
How to join PubMed Commons

    Supplemental Content

    Full text links

    Icon for Indian Academy of Sciences Icon for PubMed Central
    Loading ...
    Support Center