PCAViz: An Open-Source Python/JavaScript Toolkit for Visualizing Molecular Dynamics Simulations in the Web Browser

Molecular dynamics (MD) simulations reveal molecular motions at atomic resolution. Recent advances in high-performance computing now enable microsecond-long simulations capable of sampling a wide range of biologically relevant events. But the disk space required to store an MD trajectory increases w...

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Bibliographic Details
Published in:Journal of chemical information and modeling Vol. 59; no. 10; p. 4087
Main Authors: Pacheco, Sayuri, Kaminsky, Jesse C, Kochnev, Iurii K, Durrant, Jacob D
Format: Journal Article
Language:English
Published: United States 28.10.2019
Subjects:
Models, Chemical
Models, Molecular
Molecular Dynamics Simulation
Molecular Structure
Software
Web Browser
ISSN:1549-960X, 1549-960X
Online Access:Get more information
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Description
Summary:Molecular dynamics (MD) simulations reveal molecular motions at atomic resolution. Recent advances in high-performance computing now enable microsecond-long simulations capable of sampling a wide range of biologically relevant events. But the disk space required to store an MD trajectory increases with simulation length and system size, complicating collaborative sharing and visualization. To overcome these limitations, we created PCAViz, an open-source toolkit for sharing and visualizing MD trajectories via the web browser. PCAViz includes two components: the PCAViz Compressor, which compresses and saves simulation data; and the PCAViz Interpreter, which decompresses the data in users' browsers and feeds it to any of several browser-based molecular-visualization libraries (e.g., 3Dmol.js, NGL Viewer, etc.). An easy-to-install WordPress plugin enables "plug-and-play" trajectory visualization. PCAViz will appeal to a broad audience of researchers and educators. The source code is available at http://durrantlab.com/pcaviz/ , and the WordPress plugin is available via the official WordPress Plugin Directory.
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ISSN:1549-960X
1549-960X
DOI:10.1021/acs.jcim.9b00703