MODE-TASK: large-scale protein motion tools

Bioinformatics
Caroline RossÖzlem Tastan Bishop

Abstract

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. 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 data are available at Bioinformatics online.

References

Feb 13, 2001·Biophysical Journal·A R AtilganI Bahar
Apr 8, 2011·Bioinformatics·Ahmet BakanIvet Bahar
Sep 26, 2013·Methods in Molecular Biology·Charles C David, Donald J Jacobs
Jul 10, 2014·The Journal of Chemical Physics·Florian SittelGerhard Stock
Oct 22, 2015·Biophysical Journal·Robert T McGibbonVijay S Pande
Jan 14, 2017·Frontiers in Molecular Biosciences·Yin-Chen HsiehPatrice Koehl
Mar 18, 2017·Global Heart·David K BrownÖzlem Tastan Bishop
Jun 3, 2017·Bioinformatics·David K BrownÖzlem Tastan Bishop
Mar 1, 2018·Biophysical Journal·Caroline J RossCanan Atilgan

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Citations

Nov 7, 2019·Nucleic Acids Research·Bilal NizamiTamás Beke-Somfai
Nov 17, 2020·Frontiers in Molecular Biosciences·Haleh AbdizadehCanan Atilgan
Jan 22, 2021·International Journal of Biological Macromolecules·Shang WangXiao-Wei Yu
Nov 7, 2020·International Journal of Molecular Sciences·Seketoulie KeretsuSeung Joo Cho
May 3, 2021·BMC Bioinformatics·Charles C DavidDonald J Jacobs
Aug 28, 2021·Journal of Chemical Information and Modeling·Afrah KhairallahÖzlem Tastan Bishop
Dec 29, 2021·Chemphyschem : a European Journal of Chemical Physics and Physical Chemistry·Ann VargheseTatyana G Karabencheva-Christova

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Methods Mentioned

BETA
PCA
protein folding
MDS

Software Mentioned

LAMMPS
- TASK
Gromacs
Blue
PyMOL
ALGLIB
Tk
VMD
Python
getEigenVector

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