Journal
BIOINFORMATICS
Volume 33, Issue 17, Pages 2768-2771Publisher
OXFORD UNIV PRESS
DOI: 10.1093/bioinformatics/btx349
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Funding
- National Institutes of Health Common Fund [U41HG006941]
- National Research Foundation (NRF), South Africa [93690]
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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.
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