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Twenty-five years of nucleic acid simulations
2013
Biopolymers
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.
doi:10.1002/bip.22331
pmid:23784813
pmcid:PMC3820278
fatcat:gpvn7lvbf5hgddqbvfvwnhd42q