Dataset Information

MD-TASK: a software suite for analyzing molecular dynamics trajectories.

ABSTRACT:

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.

SUBMITTER: Brown DK

PROVIDER: S-EPMC5860072 | biostudies-literature | 2017 Sep

REPOSITORIES: biostudies-literature

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Publications

MD-TASK: a software suite for analyzing molecular dynamics trajectories.

Brown David K DK Penkler David L DL Sheik Amamuddy Olivier O Ross Caroline C Atilgan Ali Rana AR Atilgan Canan C Tastan Bishop Özlem Ö

Bioinformatics (Oxford, England) 20170901 17

<h4>Summary</h4>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, an ...[more]

PMID: 28575169

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Dataset Information

MD-TASK: a software suite for analyzing molecular dynamics trajectories.

Summary

Availability and implementation

Contact

Publications

MD-TASK: a software suite for analyzing molecular dynamics trajectories.

Similar Datasets

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