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Twenty‐five years of nucleic acid simulations
Author(s) -
Cheatham Thomas E.,
Case David A.
Publication year - 2013
Publication title -
biopolymers
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.556
H-Index - 125
eISSN - 1097-0282
pISSN - 0006-3525
DOI - 10.1002/bip.22331
Subject(s) - nucleic acid , chemistry , oligonucleotide , rna , dna , duplex (building) , perspective (graphical) , computational biology , statistical physics , physics , computer science , biochemistry , biology , artificial intelligence , gene
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.