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Title: Bringing Molecular Dynamics Simulation Data into View

Abstract

Molecular Dynamics (MD) simulations monitor time-resolved motions of macromolecules. While visualization of MD trajectories allows an instant and intuitive understanding of dynamics and function, so far mainly static representations are provided in published literature. Recent advances in browser technology may allow for the sharing of trajectories through interactive visualization on the web. We believe that by providing intuitive and interactive visualization along with related protocols and analysis data promotes understanding, reliability, and re-usability of MD simulations. Existing barriers for sharing MD simulations are discussed and emerging solutions are highlighted. We predict that interactive visualization of MD trajectories will quickly be adopted by researchers, research consortiums, journals, and funding agencies to gather and distribute results from MD simulations via the web.

Authors:
; ;
Publication Date:
Research Org.:
RCSB Protein Data Bank (United States)
Sponsoring Org.:
USDOE Office of Science (SC), Biological and Environmental Research (BER); German Research Foundation (DFG); Berlin Institute of Health (BIH); Einstein Center Digital Future; National Science Foundation (NSF); National Institutes of Health (NIH)
OSTI Identifier:
1564312
Alternate Identifier(s):
OSTI ID: 1601255
Grant/Contract Number:  
SC0019749
Resource Type:
Published Article
Journal Name:
Trends in Biochemical Sciences
Additional Journal Information:
Journal Name: Trends in Biochemical Sciences Journal Volume: 44 Journal Issue: 11; Journal ID: ISSN 0968-0004
Publisher:
Cell Press
Country of Publication:
United Kingdom
Language:
English
Subject:
59 BASIC BIOLOGICAL SCIENCES; 37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CHEMISTRY; molecular dynamics; trajectory; interactive visualization; web-based; sharing; molecular graphics

Citation Formats

Hildebrand, Peter W., Rose, Alexander S., and Tiemann, Johanna K. S. Bringing Molecular Dynamics Simulation Data into View. United Kingdom: N. p., 2019. Web. doi:10.1016/j.tibs.2019.06.004.
Hildebrand, Peter W., Rose, Alexander S., & Tiemann, Johanna K. S. Bringing Molecular Dynamics Simulation Data into View. United Kingdom. https://doi.org/10.1016/j.tibs.2019.06.004
Hildebrand, Peter W., Rose, Alexander S., and Tiemann, Johanna K. S. Wed . "Bringing Molecular Dynamics Simulation Data into View". United Kingdom. https://doi.org/10.1016/j.tibs.2019.06.004.
@article{osti_1564312,
title = {Bringing Molecular Dynamics Simulation Data into View},
author = {Hildebrand, Peter W. and Rose, Alexander S. and Tiemann, Johanna K. S.},
abstractNote = {Molecular Dynamics (MD) simulations monitor time-resolved motions of macromolecules. While visualization of MD trajectories allows an instant and intuitive understanding of dynamics and function, so far mainly static representations are provided in published literature. Recent advances in browser technology may allow for the sharing of trajectories through interactive visualization on the web. We believe that by providing intuitive and interactive visualization along with related protocols and analysis data promotes understanding, reliability, and re-usability of MD simulations. Existing barriers for sharing MD simulations are discussed and emerging solutions are highlighted. We predict that interactive visualization of MD trajectories will quickly be adopted by researchers, research consortiums, journals, and funding agencies to gather and distribute results from MD simulations via the web.},
doi = {10.1016/j.tibs.2019.06.004},
journal = {Trends in Biochemical Sciences},
number = 11,
volume = 44,
place = {United Kingdom},
year = {2019},
month = {7}
}

Journal Article:
Free Publicly Available Full Text
Publisher's Version of Record
https://doi.org/10.1016/j.tibs.2019.06.004

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Cited by: 7 works
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