PCAViz: An Open-Source Python/JavaScript Toolkit for Visualizing Molecular Dynamics Simulations in the Web Browser
| Autor: | Sayuri Pacheco, Iurii K. Kochnev, Jesse C. Kaminsky, Jacob D. Durrant |
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| Rok vydání: | 2019 |
| Předmět: |
Models
Molecular Molecular Structure 010304 chemical physics Computer science General Chemical Engineering General Chemistry Molecular Dynamics Simulation Web Browser Library and Information Sciences Python (programming language) JavaScript 01 natural sciences 0104 chemical sciences Computer Science Applications 010404 medicinal & biomolecular chemistry Molecular dynamics Open source Models Chemical Atomic resolution Computer graphics (images) 0103 physical sciences Molecular motion computer Software computer.programming_language |
| Zdroj: | Journal of Chemical Information and Modeling. 59:4087-4092 |
| ISSN: | 1549-960X 1549-9596 |
| DOI: | 10.1021/acs.jcim.9b00703 |
| Popis: | 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. |
| Databáze: | OpenAIRE |
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