MDsrv -- visual sharing and analysis of molecular dynamics simulations

TL;DR

MDsrv is a web-based tool that streamlines sharing, visualization, and analysis of molecular dynamics simulations, enabling collaborative exploration without advanced skills and supporting remote datasets and initial analyses.

Contribution

The paper introduces enhancements to MDsrv that simplify sharing, enable remote dataset access, and add initial analysis features, expanding its usability and efficiency.

Findings

Supports remote dataset visualization

Enables easy sharing with preset views

Provides initial analysis tools like RMSD

Abstract

Molecular dynamics simulation is a proven technique for computing and visualizing the time-resolved motion of macromolecules at atomic resolution. The MDsrv is a tool that streams MD trajectories and displays them interactively in web browsers without requiring advanced skills, facilitating interactive exploration and collaborative visual analysis. We have now enhanced the MDsrv to further simplify the upload and sharing of MD trajectories and improve their online viewing and analysis. With the new instance, the MDsrv simplifies the creation of sessions, which allows the exchange of MD trajectories with preset representations and perspectives. An important innovation is that the MDsrv can now access and visualize trajectories from remote datasets, which greatly expands its applicability and use, as the data no longer needs to be accessible on a local server. In addition, initial analyses such as sequence or structure alignments, distance measurements, or RMSD calculations have been implemented, which optionally support visual analysis. Finally, the MDsrv now offers a faster and more efficient visualization of even large trajectories.