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arXiv · 1711.08078

HTMoL: full-stack solution for remote access, visualization, and analysis of Molecular Dynamics trajectory data

Mauricio Carrillo-Tripp·Leonardo Alvarez-Rivera·Omar Israel Lara-Ramírez·Francisco Javier Becerra-Toledo·Adan Vega-Ramírez·Emmanuel Quijas-Valades·Eduardo González-Zavala·Julio Cesar González-Vázquez·Javier García-Vieyra·Nelly Beatriz Santoyo-Rivera·Amilcar Meneses-Viveros·Sergio Victor Chapa-Vergara
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Abstract

The field of structural bioinformatics has seen significant advances with the use of Molecular Dynamics (MD) simulations of biological systems. The MD methodology has allowed to explain and discover molecular mechanisms in a wide range of natural processes. There is an impending need to readily share the ever-increasing amount of MD data, which has been hindered by the lack of specialized tools in the past. To solve this problem, we present HTMoL, a state-of-the-art plug-in-free hardware-accelerated web application specially designed to efficiently transfer and visualize raw MD trajectory files on a web browser. Now, individual research labs can publish MD data on the Internet, or use HTMoL to profoundly improve scientific reports by including supplemental MD data in a journal publication. HTMoL can also be used as a visualization interface to access MD trajectories generated on a high-performance computer center directly. Availability: HTMoL is available free of charge for academic use. All major browsers are supported. A complete online documentation including instructions for download, installation, configuration, and examples is available at the HTMoL website http://htmol.tripplab.com. Supplementary data are available online. Corresponding author: mauricio.carrillo@cinvestav.mx

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Mauricio Carrillo-Tripp, Leonardo Alvarez-Rivera, Omar Israel Lara-Ramírez, Francisco Javier Becerra-Toledo, Adan Vega-Ramírez, Emmanuel Quijas-Valades, Eduardo González-Zavala, Julio Cesar González-Vázquez, Javier García-Vieyra, Nelly Beatriz Santoyo-Rivera, Amilcar Meneses-Viveros, Sergio Victor Chapa-Vergara. 2017-11-21. HTMoL: full-stack solution for remote access, visualization, and analysis of Molecular Dynamics trajectory data. https://doi.org/10.1007/s10822-018-0141-y

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