title: Simulating DNA by molecular dynamics: aims, methods, and validation.
abstract: The structure and dynamics of the B-DNA double helix involves subtle sequence-dependent effects which are decisive for its function, but difficult to characterize. These structural and dynamic effects can be addressed by simulations of DNA sequences in explicit solvent. Here, we present and discuss the state-of-art of B-DNA molecular dynamics simulations with the major force fields in use today. We explain why a critical analysis of the MD trajectories is required to assess their reliability, and estimate the value and limitations of these models. Overall, simulations of DNA bear great promise towards deciphering the structural and physical subtleties of this biopolymer, where much remains to be understood.
authors.affiliation: Vernalis (R&D) Ltd, Granta Park, Abington, Cambridge, UK.
authors.forename: Nicolas
authors.initials: N
authors.lastname: Foloppe
authors.forename: Marc
authors.initials: M
authors.lastname: Guéroult
authors.forename: Brigitte
authors.initials: B
authors.lastname: Hartmann
mesh_terms: D059371:DNA, B-Form / Q000737:chemistry* / Q000378:metabolism; D006027:Glycosides / Q000737:chemistry; D020407:Internet; D056004:Molecular Dynamics Simulation; D009690:Nucleic Acid Conformation; D010710:Phosphates / Q000737:chemistry; D011506:Proteins / Q000378:metabolism; D015203:Reproducibility of Results; D012984:Software; D055672:Static Electricity; D014867:Water / Q000737:chemistry
chemical_list: D059371:DNA, B-Form; D006027:Glycosides; D010710:Phosphates; D011506:Proteins; D014867:Water