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¶
Helical Base-stesp parameters¶
Major and minor grooves¶
Radius of DNA Helix¶
Backbone torsional angles¶
Example: Conformational wheel using backbone torsion angles:
Please cite the following publications:
- Xiang-Jun Lu & Wilma K. Olson (2003)3DNA: a software package for the analysis, rebuilding and visualization of three-dimensional nucleic acid structures.Nucleic Acids Res. 31(17), 5108-21.
- Rajendra Kumar and Helmut Grubmüller (2015)do_x3dna: a tool to analyze structural fluctuations of dsDNA or dsRNA from molecular dynamics simulationsBioinformatics (2015) 31 (15): 2583-2585.