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. 2017 Sep 1;33(17):2768-2771.
doi: 10.1093/bioinformatics/btx349.

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

David K Brown  1 , David L Penkler  1 , Olivier Sheik Amamuddy  1 , Caroline Ross  1 , Ali Rana Atilgan  2 , Canan Atilgan  2 , Özlem Tastan Bishop  1
Affiliations

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

David K Brown et al. Bioinformatics. .

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.

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Figures

Fig. 1
Fig. 1
Outputs for (A) Network analysis: average ΔL; average ΔBC; residue contact maps (from top to bottom); (B) DCC; (C) PRS (plot not generated by MD-TASK); (D) HIV-protease with significant regions highlighted
See this image and copyright information in PMC

References

    1. Atilgan A.R. et al. (2011) Subtle pH differences trigger single residue motions for moderating conformations of calmodulin. J. Chem. Phys., 135, - PubMed
    1. Atilgan C. et al. (2012) Network-based models as tools hinting at nonevident protein functionality. Annu. Rev. Biophys., 41, 205–225. - PubMed
    1. Atilgan C., Atilgan A.R. (2009) Perturbation-response scanning reveals ligand entry-exit mechanisms of ferric binding protein. PLoS Comput. Biol., 5, 10005–10044. - PMC - PubMed
    1. Bhakat S. et al. (2014) An integrated molecular dynamics, principal component analysis and residue interaction network approach reveals the impact of M184V mutation on HIV reverse transcriptase resistance to lamivudine. Mol. Biosyst., 10, 2215–2228. - PubMed
    1. Brandes U. (2001) A faster algorithm for betweenness centrality*. J. Math. Sociol., 25, 163–177.