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

TL;DR

HTMoL is a web-based, hardware-accelerated tool enabling efficient remote visualization and analysis of Molecular Dynamics simulation data directly in web browsers, facilitating data sharing and scientific reporting.

Contribution

This paper introduces HTMoL, a novel plug-in-free web application that allows high-performance, remote access and visualization of MD trajectories, addressing previous limitations in data sharing tools.

Findings

Supports all major browsers for broad accessibility

Enables direct visualization of MD data on high-performance computing centers

Facilitates sharing and publication of MD data online

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