title: Twenty-five years of nucleic acid simulations.
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.
authors.affiliation: Department of Medicinal Chemistry, College of Pharmacy, University of Utah, 2000 East 30 South Skaggs 105, Salt Lake City, UT, 84112.
authors.forename: Thomas E
authors.initials: TE
authors.lastname: Cheatham
authors.forename: David A
authors.initials: DA
authors.lastname: Case
mesh_terms: D003198:Computer Simulation; D004247:DNA / Q000737:chemistry; D009690:Nucleic Acid Conformation; D009841:Oligonucleotides / Q000737:chemistry; D012313:RNA / Q000737:chemistry; D013816:Thermodynamics
chemical_list: D009841:Oligonucleotides; D012313:RNA; D004247:DNA
keywords: force fields; molecular dynamics; nucleic acids