do_x3dna: a tool to analyze structural fluctuations of dsDNA or dsRNA from molecular dynamics simulations | Zendy

Rajendra Kumar | Zendy; Helmut Grubmüller | Zendy

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

Author(s) -

Rajendra Kumar,

Helmut Grubmüller

Publication year - 2015

Publication title -

bioinformatics

Language(s) - English

Resource type - Journals

SCImago Journal Rank - 3.599

H-Index - 390

eISSN - 1367-4811

pISSN - 1367-4803

DOI - 10.1093/bioinformatics/btv190

Subject(s) - python (programming language) , molecular dynamics , computer science , r package , computational science , statistical physics , software package , dna , physics , algorithm , software , biology , genetics , programming language , quantum mechanics

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.

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