CgDNA: a software package for the prediction of sequence-dependent coarse-grain free energies of B-form DNA.

ABSTRACT: cgDNA is a package for the prediction of sequence-dependent configuration-space free energies for B-form DNA at the coarse-grain level of rigid bases. For a fragment of any given length and sequence, cgDNA calculates the configuration of the associated free energy minimizer, i.e. the relative positions and orientations of each base, along with a stiffness matrix, which together govern differences in free energies. The model predicts non-local (i.e. beyond base-pair step) sequence dependence of the free energy minimizer. Configurations can be input or output in either the Curves+ definition of the usual helical DNA structural variables, or as a PDB file of coordinates of base atoms. We illustrate the cgDNA package by comparing predictions of free energy minimizers from (a) the cgDNA model,

SUBMITTER: Petkeviciute D 

PROVIDER: S-EPMC4227758 | biostudies-literature | 2014 Nov

REPOSITORIES: biostudies-literature