MDM-TASK-web: MD-TASK and MODE-TASK web server for analyzing protein dynamics

Abstract

AbstractMDM-TASK-web is the web server for the MD-TASK and MODE-TASK software suites. It simplifies the set-up required to perform and visualize results from dynamic residue network analysis, perturbation-response scanning, dynamic cross-correlation, essential dynamics and normal mode analysis. In a nutshell, the server gives access to updated versions of the tool suites, and offers new functionalities and integrated 2D/3D visualization. An embedded work-flow, integrated documentation and visualization tools shortens the number of steps to follow, starting from calculations to result visualization. The web server (available at https://mdmtaskweb.rubi.ru.ac.za/) is powered by Django and a MySQL database, and is compatible with all major web browsers. All scripts implemented in the web platform are freely available at https://github.com/RUBi-ZA/MD-TASK/tree/mdm-task-web and https://github.com/RUBi-ZA/MODE-TASK/tree/mdm-task-web.HighlightsMDM-TASK-web is the web server for highly utilized MD-TASK and MODE-TASK with updatesEight residue network centrality metrics are available to analyze static and dynamic proteinsNovel comparative essential dynamics is established to compare independent MD simulationsCommunication propensity tool to evaluate residue communication efficiency is implemented.Normal mode analysis from static and protein MD simulations is provided