Protein docking is essential for structural characterization of protein interactions. Besides providing the structure of protein complexes, modeling of proteins and their complexes is important for understanding the fundamental principles and specific aspects of protein interactions. The accuracy of protein modeling, in general, is still less than that of the experimental approaches. Thus, it is important to investigate the applicability of docking techniques to modeled proteins. We present new comprehensive benchmark sets of protein models for the development and validation of protein docking, as well as a systematic assessment of free and template‐based docking techniques on these sets. As opposed to previous studies, the benchmark sets reflect the real case modeling/docking scenario where the accuracy of the models is assessed by the modeling procedure, without reference to the native structure (which would be unknown in practical applications). We also expanded the analysis to include docking of protein pairs where proteins have different structural accuracy. The results show that, in general, the template‐based docking is less sensitive to the structural inaccuracies of the models than the free docking. The near‐native docking poses generated by the template‐based approach, typically, also have higher ranks than those produces by the free docking (although the free docking is indispensable in modeling the multiplicity of protein interactions in a crowded cellular environment). The results show that docking techniques are applicable to protein models in a broad range of modeling accuracy. The study provides clear guidelines for practical applications of docking to protein models.

中文翻译：

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对接方法在建模蛋白质中的应用。

蛋白质对接对于蛋白质相互作用的结构表征至关重要。除了提供蛋白质复合物的结构外，蛋白质及其复合物的建模对于理解蛋白质相互作用的基本原理和特定方面也很重要。一般来说，蛋白质建模的准确性仍然低于实验方法的准确性。因此，重要的是研究对接技术对建模蛋白质的适用性。我们提出了用于蛋白质对接开发和验证的新的综合蛋白质模型基准集，以及对这些集上的自由和基于模板的对接技术的系统评估。与以往的研究相反，基准集反映了真实案例建模/对接场景，其中模型的准确性由建模程序评估，而不参考原始结构（在实际应用中是未知的）。我们还扩展了分析以包括蛋白质对的对接，其中蛋白质具有不同的结构准确性。结果表明，一般来说，基于模板的对接对模型的结构不准确性比自由对接更不敏感。由基于模板的方法生成的近自然对接姿势通常也比自由对接产生的排名更高（尽管自由对接对于在拥挤的细胞环境中模拟蛋白质相互作用的多样性是必不可少的）。结果表明，对接技术适用于具有广泛建模精度的蛋白质模型。该研究为对接到蛋白质模型的实际应用提供了明确的指导。