Introduction

do_x3dna has been developed for analysis of the DNA/RNA dynamics during the molecular dynamics simulations. It consists of three main components:

  • do_x3dna — To calculate structural descriptors of DNA/RNA from MD trajectory. Also available as a stand-alone and independent VMD plugin.
  • dnaMD — Command line tool to extract and analyze the data obtained from do_x3dna for users without programming experiences.
  • dnaMD Python module — To extract and analyze the data obtained from do_x3dna for users with programming experiences.

Last Update: Oct. 2017

For Questions and Discussions, please visit: do_x3dna forum.

Release Note 2017

Features

Base-pair parameters

_images/bp_parameters.png

Base-step parameters

_images/bps_parameters.png

Helical Base-stesp parameters

_images/bph_parameters.png

Major and minor grooves

Radius of DNA Helix

Backbone torsional angles

_images/backbone_torsions.png

Example: Conformational wheel using backbone torsion angles:

_images/backbone_torsion_wheel.png

Helical axis and its curvature

Examples:

_images/p3tmm.png
  • Bending in the helical axis of a DNA in the nucleosome:
_images/p3ut9.png

Citations

Please cite the following publications:

Indices and tables