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首页> 外文期刊>Journal of Bioinformatics and Computational Biology >EasyAmber: A comprehensive toolbox to automate the molecular dynamics simulation of proteins
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EasyAmber: A comprehensive toolbox to automate the molecular dynamics simulation of proteins

机译：EasyAdber：一个综合工具箱，用于自动化蛋白质的分子动力学模拟

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Conformational plasticity of the functionally important regions and binding sites in protein/enzyme structures is one of the key factors affecting their function and interaction with substrates/ligands. Molecular dynamics (MD) can address the challenge of accounting for protein flexibility by predicting the time-dependent behavior of a molecular system. It has a potential of becoming a particularly important tool in protein engineering and drug discovery, but requires specialized training and skills, what impedes practical use by many investigators. We have developed the easyAmber - a comprehensive set of programs to automate the molecular dynamics routines implemented in the Amber package. The toolbox can address a wide set of tasks in computational biology struggling to account for protein flexibility. The automated workflow includes a complete set of steps from the initial "static" molecular model to the MD "production run": the full-atom model building, optimization/equilibration of the molecular system, classical/conventional and accelerated molecular dynamics simulations. The easyAmber implements advanced MD protocols, but is highly automated and easy-to-operate to attract a broad audience. The toolbox can be used on a personal desktop station equipped with a compatible gaming GPU-accelerator, as well as help to manage huge workloads on a powerful supercomputer. The software provides an opportunity to operate multiple simulations of different proteins at the same time, thus significantly increasing work efficiency. The easyAmber takes the molecular dynamics to the next level in terms of usability for complex processing of large volumes of data, thus supporting the recent trend away from inefficient "static" approaches in biology toward a deeper understanding of the dynamics in protein structures. The software is freely available for download at https://biokinet .belo-zersky .msu.ru/easyAmber, no login required.
机译：蛋白质/酶结构中重要功能区域和结合位点的构象可塑性是影响其功能和与底物/配体相互作用的关键因素之一。分子动力学（MD）可以通过预测分子系统的时间依赖性行为来解决解释蛋白质灵活性的挑战。它有可能成为蛋白质工程和药物发现中一个特别重要的工具，但需要专门的培训和技能，这阻碍了许多研究人员的实际使用。我们已经开发了easyAmber——一套全面的程序，用于自动化Amber软件包中实现的分子动力学例程。该工具箱可以解决计算生物学中一系列难以解释蛋白质灵活性的任务。自动化工作流程包括从最初的“静态”分子模型到MD“生产运行”的一整套步骤：全原子模型构建、分子系统的优化/平衡、经典/常规和加速分子动力学模拟。easyAmber实现了先进的MD协议，但高度自动化，易于操作，以吸引广泛的观众。该工具箱可用于配备兼容游戏GPU加速器的个人桌面工作站，也可帮助管理功能强大的超级计算机上的巨大工作负载。该软件提供了同时对不同蛋白质进行多个模拟的机会，从而显著提高了工作效率。easyAmber将分子动力学的可用性提升到了一个新的水平，可以对大量数据进行复杂处理，从而支持了最近从生物学中低效的“静态”方法转向更深入地理解蛋白质结构动力学的趋势。该软件可在以下网站免费下载：https://biokinet贝洛·泽尔斯基先生。密歇根州立大学。ru/easyAmber，无需登录。

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