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bioRxiv · 10.1101/2021.01.29.428734

MDM-TASK-web: A web platform for protein dynamic residue networks and modal analysis

Sheik Amamuddy, O.·Glenister, M.·Tastan Bishop, O.
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Abstract

MDM-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. HighlightsO_LIMDM-TASK-web is the web server for highly utilized MD-TASK and MODE-TASK with updates C_LIO_LIEight residue network centrality metrics are available to analyze static and dynamic proteins C_LIO_LINovel comparative essential dynamics is established to compare independent MD simulations C_LIO_LICommunication propensity tool to evaluate residue communication efficiency is implemented. C_LIO_LINormal mode analysis from static and protein MD simulations is provided C_LI

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Sheik Amamuddy, O., Glenister, M., Tastan Bishop, O.. 2021-02-01. MDM-TASK-web: A web platform for protein dynamic residue networks and modal analysis. https://doi.org/10.1101/2021.01.29.428734

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