Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris-Sud, Université Paris-Saclay, 91198, Gif-sur-Yvette cedex, France.
INSERM UMR-S 973, Université Paris Diderot, Sorbonne Paris Cité, RPBS, Paris 75205, France.
Nucleic Acids Res. 2018 Jul 2;46(W1):W408-W416. doi: 10.1093/nar/gky377.
Computational protein docking is a powerful strategy to predict structures of protein-protein interactions and provides crucial insights for the functional characterization of macromolecular cross-talks. We previously developed InterEvDock, a server for ab initio protein docking based on rigid-body sampling followed by consensus scoring using physics-based and statistical potentials, including the InterEvScore function specifically developed to incorporate co-evolutionary information in docking. InterEvDock2 is a major evolution of InterEvDock which allows users to submit input sequences - not only structures - and multimeric inputs and to specify constraints for the pairwise docking process based on previous knowledge about the interaction. For this purpose, we added modules in InterEvDock2 for automatic template search and comparative modeling of the input proteins. The InterEvDock2 pipeline was benchmarked on 812 complexes for which unbound homology models of the two partners and co-evolutionary information are available in the PPI4DOCK database. InterEvDock2 identified a correct model among the top 10 consensus in 29% of these cases (compared to 15-24% for individual scoring functions) and at least one correct interface residue among 10 predicted in 91% of these cases. InterEvDock2 is thus a unique protein docking server, designed to be useful for the experimental biology community. The InterEvDock2 web interface is available at http://bioserv.rpbs.univ-paris-diderot.fr/services/InterEvDock2/.
计算蛋白质对接是一种预测蛋白质-蛋白质相互作用结构的强大策略，为研究大分子相互作用提供了关键的见解。我们之前开发了 InterEvDock，这是一个基于刚体采样的从头开始蛋白质对接服务器，随后使用基于物理和统计势的共识评分，包括专门开发的 InterEvScore 函数，用于在对接中纳入共进化信息。InterEvDock2 是 InterEvDock 的重大演进，允许用户提交输入序列（不仅是结构）和多聚体输入，并根据关于相互作用的先前知识为成对对接过程指定约束。为此，我们在 InterEvDock2 中添加了模块，用于输入蛋白质的自动模板搜索和比较建模。InterEvDock2 管道在 PPI4DOCK 数据库中可用的 812 个复合物上进行了基准测试，这些复合物的两个伴侣的未结合同源模型和共进化信息可用。在这些情况下，InterEvDock2 在 29%的情况下在前 10 个共识中确定了正确的模型（相比之下，单个评分函数为 15-24%），并且在这些情况下的 91%中，至少有一个正确的接口残基在预测的 10 个中。因此，InterEvDock2 是一个独特的蛋白质对接服务器，旨在为实验生物学界提供有用的服务。InterEvDock2 的网络界面可在 http://bioserv.rpbs.univ-paris-diderot.fr/services/InterEvDock2/ 获得。
