do_x3dna: A tool to analyze structural fluctuations of dsDNA or dsRNA from 
molecular dynamics simulations.

Kumar, R.; Grubmüller, H.

doi:10.1093/bioinformatics/btv190

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do_x3dna: A tool to analyze structural fluctuations of dsDNA or dsRNA from molecular dynamics simulations.

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Kumar, R.
Department of Theoretical and Computational Biophysics, MPI for Biophysical Chemistry, Max Planck Society;

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Grubmüller, H.
Department of Theoretical and Computational Biophysics, MPI for Biophysical Chemistry, Max Planck Society;

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http://bioinformatics.oxfordjournals.org/cgi/pmidlookup?view=long&pmid=25838463
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Citation

Kumar, R., & Grubmüller, H. (2015). do_x3dna: A tool to analyze structural fluctuations of dsDNA or dsRNA from molecular dynamics simulations. Bioinformatics, 31(15), 2583-2585. doi:10.1093/bioinformatics/btv190.

Cite as: https://hdl.handle.net/11858/00-001M-0000-0026-B010-B

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.