Targets in the protein docking experiment CAPRI (Critical Assessment of Predicted Interactions) generally present new challenges and contribute to new developments in methodology. In rounds 38 to 45 of CAPRI, most targets could be effectively predicted using template‐based methods. However, the server ClusPro required structures rather than sequences as input, and hence we had to generate and dock homology models. The available templates also provided distance restraints that were directly used as input to the server. We show here that such an approach has some advantages. Free docking with template‐based restraints using ClusPro reproduced some interfaces suggested by weak or ambiguous templates while not reproducing others, resulting in correct server predicted models. More recently we developed the fully automated ClusPro TBM server that performs template‐based modeling and thus can use sequences rather than structures of component proteins as input. The performance of the server, freely available for noncommercial use at https://tbm.cluspro.org, is demonstrated by predicting the protein‐protein targets of rounds 38 to 45 of CAPRI.

中文翻译：

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CAPRI 第 38 至 45 轮中的 ClusPro：将基于模板的方法与自由对接相结合。

蛋白质对接实验 CAPRI（预测相互作用的关键评估）中的目标通常会带来新的挑战，并有助于方法学的新发展。在 CAPRI 的第 38 至 45 轮中，大多数目标可以使用基于模板的方法进行有效预测。然而，服务器 ClusPro 需要结构而不是序列作为输入，因此我们必须生成和对接同源模型。可用模板还提供了直接用作服务器输入的距离限制。我们在这里展示了这种方法有一些优点。使用 ClusPro 与基于模板的约束的自由对接重现了弱模板或模棱两可的模板建议的一些接口，而不会重现其他接口，从而产生正确的服务器预测模型。最近，我们开发了全自动 ClusPro TBM 服务器，它执行基于模板的建模，因此可以使用序列而不是组分蛋白质的结构作为输入。服务器的性能可在 https://tbm.cluspro.org 上免费用于非商业用途，通过预测 CAPRI 第 38 至 45 轮的蛋白质-蛋白质目标来证明。