MODE-TASK: large-scale protein motion tools

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 Netwo...

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Detalles Bibliográficos
Autores principales: Ross, Caroline, Nizami, Bilal, Glenister, Michael, Sheik Amamuddy, Olivier, Atilgan, Ali Rana, Atilgan, Canan, Tastan Bishop, Özlem
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Oxford University Press 2018
Materias:
Applications Notes
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6198866/
https://www.ncbi.nlm.nih.gov/pubmed/29850770
http://dx.doi.org/10.1093/bioinformatics/bty427
Descripción
Sumario: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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