MDM-TASK-web: MD-TASK and MODE-TASK web server for analyzing protein dynamics.
MDM-TASK-web: MD-TASK and MODE-TASK web server for analyzing protein dynamics.
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DOI：
10.1016/j.csbj.2021.08.043
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发表时间：
2021
影响因子：
6
通讯作者：
Tastan Bishop Ö
中科院分区：
文献类型：
--
作者：
Sheik Amamuddy O;Glenister M;Tshabalala T;Tastan Bishop Ö
MD-task和MODE-task的Web服务器，带有新工具和更新。八个动态残基网络中心性度量用于分析蛋白质分子动力学，扩展为静态蛋白质。用于改进相关蛋白质的独立分子动力学模拟的比较基本动力学。一种用于评估剩余通信效率的通信倾向工具。从静态结构和分子动力学模拟分析蛋白质的简正模。Web服务器MDM-task-web结合了MD-task和MODE-task软件套件，这些软件套件针对静态和全原子MD模拟蛋白质的粗粒度分析，使用各种非常规方法，例如动态残基网络分析，扰动响应扫描，动态互相关，基本动力学和正常模式分析。总而言之，这些工具允许探索蛋白质动力学在不同层次的细节，跨越单一残基扰动和加权接触网络表示，全球残留中心测量和全球蛋白质运动的调查。通常，在设计用于研究内在和外在蛋白质扰动（例如由变构和正构配体、蛋白质结合、温度、pH和突变诱导）的分子动力学模拟之后，这种工具的选择可用于进一步描述蛋白质动力学。这可能导致发现参与生物过程的关键残留物，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。更新了工具套件中的几个脚本，还添加了新的脚本，并通过Web界面与2D/3D可视化集成。嵌入式工作流程、集成的文档和可视化工具缩短了从计算到结果可视化的步骤数量。Django驱动的Web服务器（可在https：//mdmtaskweb.rubi.ru.ac.za/获得）与所有主要的Web浏览器兼容。在Web平台中实现的所有脚本都可以在https://github.com/RUBi-ZA/MD-TASK/tree/mdm-task-web和https://github.com/RUBi-ZA/MODE-TASK/tree/mdm-task-web上免费获得。
Web server for MD-TASK and MODE-TASK, with new tools and updates. Eight dynamic residue network centrality metrics for analyzing protein molecular dynamics, extended for static proteins. Comparative essential dynamics for improved comparison of independent molecular dynamic simulations of related proteins. A communication propensity tool for evaluating residue communication efficiency. Normal mode analysis of proteins from static structures and molecular dynamic simulations. 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 shorten 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.
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影响因子：
3.7
作者：
Brown DK;Sheik Amamuddy O;Tastan Bishop Ö
通讯作者：
Tastan Bishop Ö
影响因子：
4.6
作者：
Amusengeri, Arnold;Tata, Rolland Bantar;Bishop, Ozlem Tastan
通讯作者：
Bishop, Ozlem Tastan
在生理温度下完整的膜模型中，Notch-和C83与γ-分泌酶的并排比较。
影响因子：
3.9
作者：
通讯作者：
--
影响因子：
5
作者：
Khairallah A;Ross CJ;Tastan Bishop Ö
通讯作者：
Tastan Bishop Ö
DOI：
10.1007/978-1-62703-658-0_11
发表时间：
2014
期刊：
Methods in molecular biology (Clifton, N.J.)
影响因子：
--
作者：
David CC;Jacobs DJ
通讯作者：
Jacobs DJ