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MDM-TASK-web: MD-TASK and MODE-TASK web server for analyzing protein dynamics
Computational and Structural Biotechnology Journal ( IF 6 ) Pub Date : 2021-09-02 , DOI: 10.1016/j.csbj.2021.08.043
Olivier Sheik Amamuddy 1 , Michael Glenister 1 , Thulani Tshabalala 1 , Özlem Tastan Bishop 1
Affiliation  

The web server, MDM-TASK-web, combines the MD-TASK and MODE-TASK software suites, which are aimed at the coarse-grained analysis of static and all-atom MD-simulated proteins, using a variety of non-conventional approaches, such as dynamic residue network analysis, perturbation-response scanning, dynamic cross-correlation, essential dynamics and normal mode analysis. Altogether, these tools allow for the exploration of protein dynamics at various levels of detail, spanning single residue perturbations and weighted contact network representations, to global residue centrality measurements and the investigation of global protein motion Typically, following molecular dynamic simulations designed to investigate intrinsic and extrinsic protein perturbations (for instance induced by allosteric and orthosteric ligands, protein binding, temperature, pH and mutations), this selection of tools can be used to further describe protein dynamics. This may lead to the discovery of key residues involved in biological processes, such as drug resistance. The server simplifies the set-up required for running these tools and visualizing their results. Several scripts from the tool suites were updated and new ones were also added and integrated with 2D/3D visualization via the web interface. An embedded work-flow, integrated documentation and visualization tools shortens the number of steps to follow, starting from calculations to result visualization. The Django-powered web server (available at https://mdmtaskweb.rubi.ru.ac.za/) 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.



中文翻译:

MDM-TASK-web:用于分析蛋白质动态的 MD-TASK 和 MODE-TASK Web 服务器

Web服务器MDM-TASK-web结合了MD-TASK和MODE-TASK软件套件,旨在使用各种非常规方法对静态和全原子MD模拟蛋白质进行粗粒度分析,如动态残差网络分析、扰动响应扫描、动态互相关、本质动力学和简正模态分析。总而言之,这些工具允许在不同细节水平上探索蛋白质动力学,涵盖单个残基扰动和加权接触网络表示,到全局残基中心性测量和全局蛋白质运动的研究通常,遵循旨在研究内在和动态的分子动态模拟外在蛋白质扰动(例如由变构和正构配体、蛋白质结合、温度、pH 和突变引起的),这种工具选择可用于进一步描述蛋白质动力学。这可能导致发现生物过程中涉及的关键残基,例如耐药性。服务器简化了运行这些工具和可视化其结果所需的设置。工具套件中的多个脚本已更新,还添加了新脚本,并通过 Web 界面与 2D/3D 可视化集成。嵌入式工作流程、集成文档和可视化工具缩短了从计算到结果可视化的步骤数。Django 支持的 Web 服务器(可在https://mdmtaskweb.rubi.ru.ac.za/获取)与所有主要 Web 浏览器兼容。Web 平台中实现的所有脚本均可在https://github.com/RUBi-ZA/MD-TASK/tree/mdm-task-webhttps://github.com/RUBi-ZA/MODE-TASK免费获取/tree/mdm-task-web

更新日期:2021-09-02
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