• MD DaVis: interactive data vis...

Treffer: MD DaVis: interactive data visualization of protein molecular dynamics.

Title:
MD DaVis: interactive data visualization of protein molecular dynamics.
Authors:
Maity D; IISc Mathematics Initiative, Department of Mathematics, Indian Institute of Science, Bangalore 560012, India., Pal D; Department of Computational and Data Sciences, Indian Institute of Science, Bangalore 560012, India.
Source:
Bioinformatics (Oxford, England) [Bioinformatics] 2022 Jun 13; Vol. 38 (12), pp. 3299-3301.
Publication Type:
Journal Article; Research Support, Non-U.S. Gov't
Language:
English
Journal Info:
Publisher: Oxford University Press Country of Publication: England NLM ID: 9808944 Publication Model: Print Cited Medium: Internet ISSN: 1367-4811 (Electronic) Linking ISSN: 13674803 NLM ISO Abbreviation: Bioinformatics Subsets: MEDLINE
Imprint Name(s):
Original Publication: Oxford : Oxford University Press, c1998-
MeSH Terms:
Molecular Dynamics Simulation* , Data Visualization*, Software ; Proteins
Grant Information:
JRF 09/079(2650)/2015-EMR-I Council of Scientific & Industrial Research; Department of Biotechnology [through the Bioengineering and Biodesign Initiative Phase 2 at the Indian Institute of Science
Substance Nomenclature:
0 (Proteins)
Entry Date(s):
Date Created: 20220509 Date Completed: 20221114 Latest Revision: 20221209
Update Code:
20250114
DOI:
10.1093/bioinformatics/btac314
PMID:
35532115
Database:
MEDLINE

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Summary: Molecular dynamics (MD) simulations have become an integral part of biomolecular study. Most MD software suites do not include analysis tools and those which do create very basic visualizations. Molecular Dynamics Data Visualizer (MD DaVis) is a python package developed to facilitate quick comparative analysis of MD trajectories of similar proteins or the same protein under different conditions. MD DaVis can quickly generate interactive visualization from molecular dynamics trajectories with a few simple steps. Interactive plots eliminate the need to make multiple plots for comparison, improving productivity and saving time.
Availability and Implementation: MD DaVis is an open-source Python 3 package (https://pypi.org/project/md-davis/) distributed under MIT license. The source code is available at https://github.com/djmaity/md-davis or https://doi.org/10.5281/zenodo.6227047.
Supplementary Information: Supplementary data are available at Bioinformatics online.
(© The Author(s) 2022. Published by Oxford University Press. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.)