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. 2018 Nov 1;34(21):3759-3763.
doi: 10.1093/bioinformatics/bty427.

MODE-TASK: large-scale protein motion tools

Caroline Ross  1 , Bilal Nizami  1 , Michael Glenister  1 , Olivier Sheik Amamuddy  1 , Ali Rana Atilgan  2 , Canan Atilgan  2 , Özlem Tastan Bishop  1
Affiliations

MODE-TASK: large-scale protein motion tools

Caroline Ross et al. Bioinformatics. .

Abstract

Summary: MODE-TASK, a novel and versatile software suite, comprises Principal Component Analysis, Multidimensional Scaling, and t-Distributed Stochastic Neighbor Embedding techniques using Molecular Dynamics trajectories. MODE-TASK also includes a Normal Mode Analysis tool based on Anisotropic Network Model so as to provide a variety of ways to analyse and compare large-scale motions of protein complexes for which long MD simulations are prohibitive. Beside the command line function, a GUI has been developed as a PyMOL plugin.

Availability and implementation: MODE-TASK is open source, and available for download from https://github.com/RUBi-ZA/MODE-TASK. It is implemented in Python and C++. It is compatible with Python 2.x and Python 3.x and can be installed by Conda.

Supplementary information: Supplementary data are available at Bioinformatics online.

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Figures

Fig. 1.
Fig. 1.
MODE-TASK visual outputs. Dimension reduction by PCA for WT (A.1) and mutant (A.2), presented per MD time point
See this image and copyright information in PMC

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