Computational design of binding sites in proteins remains difficult, in part due to limitations in our current ability to sample backbone conformations that enable precise and accurate geometric positioning of side chains during sequence design. Here we present a benchmark framework for comparison between flexible-backbone design methods applied to binding interactions. We quantify the ability of different flexible backbone design methods in the widely used protein design software Rosetta to recapitulate observed protein sequence profiles assumed to represent functional protein/protein and protein/small molecule binding interactions. The CoupledMoves method, which combines backbone flexibility and sequence exploration into a single acceptance step during the sampling trajectory, better recapitulates observed sequence profiles than the BackrubEnsemble and FastDesign methods, which separate backbone flexibility and sequence design into separate acceptance steps during the sampling trajectory. Flexible-backbone design with the CoupledMoves method is a powerful strategy for reducing sequence space to generate targeted libraries for experimental screening and selection.

中文翻译：

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Rosetta柔性骨干计算蛋白设计方法对结合相互作用的比较。

蛋白质中结合位点的计算设计仍然很困难，部分原因是我们目前对骨架构象进行采样的能力受到限制，这些能力使序列设计过程中侧链的精确和精确的几何定位成为可能。在这里，我们提供了一个基准框架，用于比较应用于绑定交互的灵活骨干设计方法。我们在广泛使用的蛋白质设计软件Rosetta中量化不同灵活骨架设计方法的能力，以概括观察到的蛋白质序列概况，这些概况假设代表功能性蛋白质/蛋白质和蛋白质/小分子结合相互作用。CoupledMoves方法将骨干灵活性和序列探索结合到了采样轨迹中的单个接受步骤中，与BackrubEnsemble和FastDesign方法相比，该方法更好地重现了观察到的序列概况，后者将主干灵活性和序列设计分离为采样轨迹中的独立接受步骤。使用CoupledMoves方法的灵活骨干设计是减少序列空间以生成用于实验筛选和选择的目标文库的强大策略。