Twenty-five years of nucleic acid simulations

Thomas E. Cheatham, David A. Case
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