MODE-TASK: large-scale protein motion tools
Bioinformatics, 2018•academic.oup.com
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�…
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�…
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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