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.belozersky.msu.ru/easyAmber, no login required.

中文翻译：

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EasyAmber：自动化蛋白质分子动力学模拟的综合工具箱

蛋白质/酶结构中功能重要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。我们开发了 easyAmber——一套全面的程序，用于自动化 Amber 包中实施的分子动力学例程。该工具箱可以解决计算生物学中努力解释蛋白质灵活性的一系列广泛任务。自动化工作流程包括从初始“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，但高度自动化且易于操作以吸引广泛的受众。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，并有助于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次模拟的机会，从而显着提高了工作效率。easyAmber 在处理大量数据的复杂性方面将分子动力学提升到了一个新的水平，从而支持了最近的趋势，即从生物学中低效的“静态”方法转向更深入地了解蛋白质结构的动力学。该软件可在 https://biokinet.belozersky.msu.ru/easyAmber 免费下载，无需登录。