Article detail · 2018
MODE-TASK: large-scale protein motion tools
- Year
- 2018
- Type
- article
Data source split
- YÖKSİS YÖKSİS article record
- YÖKSİS venue Bioinformatics
- Catalog match (ISSN) Bioinformatics
- OpenAlex OpenAlex enrichment (abstract, citations, topics)
Abstract
OpenAlex · English
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.
Topics
Citations
OpenAlex cited_by_count. Not a WoS or Scopus citation count; those sources have no separate column here.
57 citations
OpenAlex cited_by_count (cache / database)
6 publications in the local catalog that cite this work (OpenAlex reference match; not the full global list).
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- Computational Methods for Efficient Sampling of Protein Landscapes and Disclosing Allosteric Regions 2018
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- A coarse-grained methodology identifies intrinsic mechanisms that dissociate interacting protein pairs 2020