Progress in technology and algorithms throughout the past decade has transformed the field of protein design and engineering. Computational approaches have become well-engrained in the processes of tailoring proteins for various biotechnological applications. Many tools and methods are developed and upgraded each year to satisfy the increasing demands and challenges of protein engineering. To help protein engineers and bioinformaticians navigate this emerging wave of dedicated software, we have critically evaluated recent additions to the toolbox regarding their application for semi-rational and rational protein engineering. These newly developed tools identify and prioritize hotspots and analyze the effects of mutations for a variety of properties, comprising ligand binding, protein–protein and protein–nucleic acid interactions, and electrostatic potential. We also discuss notable progress to target elusive protein dynamics and associated properties like ligand-transport processes and allosteric communication. Finally, we discuss several challenges these tools face and provide our perspectives on the further development of readily applicable methods to guide protein engineering efforts.

中文翻译：

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用于工程蛋白质功能的用户友好计算工具的最新进展。

过去十年中技术和算法的进步改变了蛋白质设计和工程领域。在为各种生物技术应用定制蛋白质的过程中，计算方法已经根深蒂固。许多工具和方法每年都在开发和升级，以满足蛋白质工程日益增长的需求和挑战。为了帮助蛋白质工程师和生物信息学家驾驭这一新兴的专用软件浪潮，我们批判性地评估了工具箱中最近添加的关于它们在半理性和理性蛋白质工程中的应用。这些新开发的工具识别和优先考虑热点，并分析突变对各种特性的影响，包括配体结合、蛋白质 - 蛋白质和蛋白质 - 核酸相互作用，和静电势。我们还讨论了针对难以捉摸的蛋白质动力学和相关特性（如配体转运过程和变构通信）的显着进展。最后，我们讨论了这些工具面临的几个挑战，并提供了我们对进一步开发易于应用的方法来指导蛋白质工程工作的看法。