.. |3DNA package| raw:: html

3DNA package

.. |mitochondiral DNA| raw:: html

mitochondiral DNA

.. |do_x3dna homepage| raw:: html

do_x3dna homepage

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 <http://do-x3dna.readthedocs.io/en/latest/do_x3dna_usage.html>`_
  --- To calculate structural descriptors of DNA/RNA from MD trajectory.
  Also available as a stand-alone and independent
  `VMD plugin <http://do-x3dna.readthedocs.io/en/latest/vmd_plugin.html>`_.

* `dnaMD <http://do-x3dna.readthedocs.io/en/latest/dnaMD_usage.html>`_
  --- Command line tool to extract and analyze the data obtained from do_x3dna
  for **users without programming experiences**.

* `dnaMD Python module <http://do-x3dna.readthedocs.io/en/latest/api_summary.html>`_
  --- To extract and analyze the data obtained from do_x3dna for
  **users with programming experiences**.

DSSR-X3DNA is incompatible with do_x3dna. Please use original 3DNA packacge. This could be dowloaded from by 3DNA forum <http://forum.x3dna.org/site-announcements/download-instructions/>_.

Last Update: Nov. 2023

For detailed documentation about the do_x3dna, please visit: |do_x3dna homepage|.

For Questions and Discussions, please visit: do_x3dna forum <https://groups.google.com/forum/#!forum/do_x3dna>_.

Release Note 2023

• do_x3dna <http://do-x3dna.readthedocs.io/en/latest/do_x3dna_usage.html>_ can be compiled and used with GROMACS-2023.x versions.

• Support for older GROMACS (4.5.x, 4.6.x, 5.0.x, 5.1.x, 2016.x and 2018.x) is removed.

• For above listed GROMACS version, the code is available in 2018 git branch. Please use git checkout 2018 to use this version.

Release Note 2018

• do_x3dna <http://do-x3dna.readthedocs.io/en/latest/do_x3dna_usage.html>_ can be compiled and used with GROMACS-2018.x versions.

• Added new dnaMD tools <http://do-x3dna.readthedocs.io/en/latest/dnaMD_usage.html#commands-table>_

• Added support to calculate both global and local Elastic properties <http://do-x3dna.readthedocs.io/en/latest/about_dna_elasticity.html>_

• Added tutorials to calculate elastic properties and deformation energy using dnaMD tool <http://do-x3dna.readthedocs.io/en/latest/global_elasticity.html>_ and dnaMD Python module <http://do-x3dna.readthedocs.io/en/latest/notebooks/calculate_elasticity_tutorial.html>_.

Release Note 2017

• do_x3dna <http://do-x3dna.readthedocs.io/en/latest/do_x3dna_usage.html>_ can be compiled and used with GROMACS 4.5.x, 4.6.x, 5.0.x, 5.1.x, and 2016.x versions.

• do_x3dna VMD plugin <http://do-x3dna.readthedocs.io/en/latest/vmd_plugin.html>_

• More user friendly --- dnaMD <http://do-x3dna.readthedocs.io/en/latest/dnaMD_usage.html>_ tools to analyze do_x3dna data <http://do-x3dna.readthedocs.io/en/latest/do_x3dna_usage.html#output-files-table>_ --- No programming experiences needed now to analyze do_x3dna data.

• Speed up dnaMD analysis with HDF5 file <http://do-x3dna.readthedocs.io/en/latest/using_hdf5.html>_

Citations

Please cite the follwoing 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 simulations <https://doi.org/10.1093/bioinformatics/btv190>_ | Bioinformatics (2015) 31 (15): 2583-2585.