MD-TASK
Computational Tool
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General Information
DescriptionA software suite for analyzing molecular dynamics trajectories
Homepagehttps://github.com/RUBi-ZA/MD-TASK
Publications
MD-TASK: a software suite for analyzing molecular dynamics trajectories
David K. Brown; David L. Penkler; Olivier Sheik Amamuddy; Caroline Ross; Ali Rana Atilgan; Canan Atilgan; Özlem Tastan Bishop
Summary: Molecular dynamics (MD) determines the physical motions of atoms of a biological macromolecule in a cell-like environment and is an important method in structural bioinformatics. Traditionally, measurements such as root mean square deviation, root mean square fluctuation, radius of gyration, and various energy measures have been used to analyze MD simulations. Here, we present MD-TASK, a novel software suite that employs graph theory techniques, perturbation response scanning, and dynamic cross-correlation to provide unique ways for analyzing MD trajectories.
Availability and implementation: MD-TASK has been open-sourced and is available for download from https://github.com/RUBi-ZA/MD-TASK, implemented in Python and supported on Linux/Unix.
Contact: o.tastanbishop@ru.ac.za
DOI: https://doi.org/10.1093/bioinformatics/btx349
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