MODE-TASK: Large-scale protein motion tools

Ross, Caroline J; Nizami, B; Glenister, M; Amamuddy, Olivier S; Atilgan, Ali R; Atilgan, Canan; Tastan Bishop, Özlem

Title: MODE-TASK: Large-scale protein motion tools
Creator: Ross, Caroline J
Creator: Nizami, B
Creator: Glenister, M
Creator: Amamuddy, Olivier S
Creator: Atilgan, Ali R
Creator: Atilgan, Canan
Creator: Tastan Bishop, Özlem
Date Issued: 2018
Date: 2018
Type: text
Type: article
Identifier: http://hdl.handle.net/10962/125206
Identifier: vital:35746
Identifier: http://dx.doi.org/10.1101/217505
Description: Conventional analysis of molecular dynamics (MD) trajectories may not identify global motions of macromolecules. Normal Mode Analysis (NMA) and Principle Component Analysis (PCA) are two popular methods to quantify large-scale motions, and find the “essential motions”; and have been applied to problems such as drug resistant mutations (Nizami et al., 2016) and viral capsid expansion (Hsieh et al., 2016). MODE-TASK is an array of tools to analyse and compare protein dynamics obtained from MD simulations and/or coarse grained elastic network models. Users may perform standard PCA, kernel and incremental PCA (IPCA). Data reduction techniques (Multidimensional Scaling (MDS) and t-Distributed Stochastics Neighbor Embedding (t-SNE)) are implemented. Users may analyse normal modes by constructing elastic network models (ENMs) of a protein complex. A novel coarse graining approach extends its application to large biological assemblies.
Format: 2 pages
Format: pdf
Language: English
Relation: Bioinformatics
Relation: Ross, C., Nizami, B., Glenister, M., Sheik Amamuddy, O., Atilgan, A.R., Atilgan, C. and Tastan Bishop, Ö., 2018. MODE-TASK: large-scale protein motion tools. Bioinformatics, 34(21), pp.3759-3763
Relation: Bioinformatics volume 34 number 21 3759 3763 2018 1367-4803
Rights: Bioinformatics
Rights: Use of this resource is governed by the terms and conditions of the bioRxiv Open Access Statement (https://www.biorxiv.org/about-biorxiv)

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Tastan Bishop, Ozlem (Prof)

RU Research Unit in Bioinformatics (RUBi)

RU Department of Biochemistry, Microbiology and Biotechnology

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