title: do_x3dna: a tool to analyze structural fluctuations of dsDNA or dsRNA from molecular dynamics simulations.
abstract: The do_x3dna package has been developed to analyze the structural fluctuations of DNA or RNA during molecular dynamics simulations. It extends the capability of the 3DNA package to GROMACS MD trajectories and includes new methods to calculate the global-helical axis of DNA and bending fluctuations during simulations. The package also includes a Python module dnaMD to perform and visualize statistical analyses of complex data obtained from the trajectories.
authors.affiliation: Department of Theoretical and Computational Biophysics, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, Göttingen 37077, Germany.
authors.forename: Rajendra
authors.initials: R
authors.lastname: Kumar
authors.affiliation: Department of Theoretical and Computational Biophysics, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, Göttingen 37077, Germany.
authors.forename: Helmut
authors.initials: H
authors.lastname: Grubmüller
mesh_terms: D004247:DNA / Q000737:chemistry*; D006801:Humans; D056004:Molecular Dynamics Simulation; D009707:Nucleosomes / Q000737:chemistry*; D012330:RNA, Double-Stranded / Q000737:chemistry*; D012984:Software
chemical_list: D009707:Nucleosomes; D012330:RNA, Double-Stranded; D004247:DNA