Department of Applied Mathematics and Statistics, Stony Brook University, Stony Brook, New York, USA.
Laufer Center for Physical and Quantitative Biology, Stony Brook University, Stony Brook, New York, USA.
Proteins. 2020 Aug;88(8):1082-1090. doi: 10.1002/prot.25887. Epub 2020 Mar 23.
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.
在蛋白质对接实验 CAPRI（相互作用预测的关键评估）中，目标通常会带来新的挑战，并为方法学的新发展做出贡献。在 CAPRI 的第 38 至 45 轮中，大多数目标都可以使用基于模板的方法进行有效预测。然而，ClusPro 服务器需要的是结构而不是序列作为输入，因此我们不得不生成和对接同源模型。可用的模板还提供了距离约束，这些约束直接作为输入提供给服务器。我们在这里表明，这种方法具有一些优势。使用 ClusPro 进行基于模板的自由对接可以再现一些由弱模板或不明确模板提示的界面，而不会再现其他界面，从而得到正确的服务器预测模型。最近，我们开发了完全自动化的 ClusPro TBM 服务器，它可以进行基于模板的建模，因此可以使用组成蛋白质的序列而不是结构作为输入。该服务器的性能可通过预测 CAPRI 的第 38 至 45 轮的蛋白质-蛋白质目标来证明，该服务器可在非商业用途免费使用，网址为 https://tbm.cluspro.org。
