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Biopolymers. 2013 Dec;99(12):969-77. doi: 10.1002/bip.22331.

Twenty-five years of nucleic acid simulations.

Author information

1
Department of Medicinal Chemistry, College of Pharmacy, University of Utah, 2000 East 30 South Skaggs 105, Salt Lake City, UT, 84112.

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.

KEYWORDS:

force fields; molecular dynamics; nucleic acids

PMID:
23784813
PMCID:
PMC3820278
DOI:
10.1002/bip.22331
[Indexed for MEDLINE]
Free PMC Article
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