Twenty-five years of nucleic acid simulations

Authors

  • Thomas E. Cheatham III,

    1. Department of Medicinal Chemistry, College of Pharmacy, University of Utah, Salt Lake City, UT
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  • David A. Case

    Corresponding author
    1. BioMaPS Institute for Quantitative Biology, Rutgers University, Piscataway, NJ
    2. Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, NJ
    • Department of Medicinal Chemistry, College of Pharmacy, University of Utah, Salt Lake City, UT
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  • This article was originally published online as an accepted preprint. The “Published Online” date corresponds to the preprint version. You can request a copy of the preprint by emailing the Biopolymers editorial office at biopolymers@wiley.com

Correspondence to: David A. Case; e-mail: case@biomaps.rutgers.edu

ABSTRACT

We present a brief, and largely personal, history of computer simulations of DNA and RNA oligonucleotides, with an emphasis on duplex structures and the Amber force fields. Both explicit and implicit solvent models are described, and methods for estimating structures, thermodynamics and mechanical properties of duplexes are illustrated. This overview, covering about two decades of work, provides a perspective for a discussion of prospects and obstacles for future simulations of RNA and DNA. © 2013 Wiley Periodicals, Inc. Biopolymers 99: 969–977, 2013.

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