Comparative docking is based on experimentally determined structures of protein‐protein complexes (templates), following the paradigm that proteins with similar sequences and/or structures form similar complexes. Modeling utilizing structure similarity of target monomers to template complexes significantly expands structural coverage of the interactome. Template‐based docking by structure alignment can be performed for the entire structures or by aligning targets to the bound interfaces of the experimentally determined complexes. Systematic benchmarking of docking protocols based on full and interface structure alignment showed that both protocols perform similarly, with top 1 docking success rate 26%. However, in terms of the models' quality, the interface‐based docking performed marginally better. The interface‐based docking is preferable when one would suspect a significant conformational change in the full protein structure upon binding, for example, a rearrangement of the domains in multidomain proteins. Importantly, if the same structure is selected as the top template by both full and interface alignment, the docking success rate increases 2‐fold for both top 1 and top 10 predictions. Matching structural annotations of the target and template proteins for template detection, as a computationally less expensive alternative to structural alignment, did not improve the docking performance. Sophisticated remote sequence homology detection added templates to the pool of those identified by structure‐based alignment, suggesting that for practical docking, the combination of the structure alignment protocols and the remote sequence homology detection may be useful in order to avoid potential flaws in generation of the structural templates library.

中文翻译：

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如何选择用于蛋白质复合物建模的模板：基于基准模板对接的见解。

比较对接基于实验确定的蛋白质-蛋白质复合物（模板）结构，遵循具有相似序列和/或结构的蛋白质形成相似复合物的范式。利用目标单体与模板复合物的结构相似性进行建模显着扩大了相互作用组的结构覆盖范围。通过结构对齐的基于模板的对接可以对整个结构进行，也可以通过将目标与实验确定的复合物的结合界面对齐。基于完整和接口结构对齐的对接协议的系统基准测试表明，两种协议的性能相似，前 1 名对接成功率为 26%。然而，就模型质量而言，基于界面的对接表现略好。当人们怀疑结合后整个蛋白质结构发生显着的构象变化时，基于界面的对接是优选的，例如，多域蛋白质中结构域的重排。重要的是，如果通过完全对齐和界面对齐选择相同的结构作为顶部模板，则前 1 和前 10 预测的对接成功率增加 2 倍。匹配用于模板检测的目标蛋白和模板蛋白的结构注释，作为结构对齐的计算成本较低的替代方案，并没有提高对接性能。复杂的远程序列同源性检测将模板添加到通过基于结构的比对识别的模板库中，这表明对于实际对接，