Program in Bioinformatics and Integrative Biology, University of Massachusetts Medical School, Worcester, Massachusetts.
Proteins. 2020 Aug;88(8):1050-1054. doi: 10.1002/prot.25873. Epub 2020 Feb 8.
We report docking performance on the six targets of Critical Assessment of PRedicted Interactions (CAPRI) rounds 39-45 that involved heteromeric protein-protein interactions and had the solved structures released since the rounds were held. Our general strategy involved protein-protein docking using ZDOCK, reranking using IRAD, and structural refinement using Rosetta. In addition, we made extensive use of experimental data to guide our docking runs. All the experimental information at the amino-acid level proved correct. However, for two targets, we also used protein-complex structures as templates for modeling interfaces. These resulted in incorrect predictions, presumably due to the low sequence identity between the targets and templates. Albeit a small number of targets, the performance described here compared somewhat less favorably with our previous CAPRI reports, which may be due to the CAPRI targets being increasingly challenging.
我们报告了在第 39-45 轮 Critical Assessment of PRedicted Interactions（CAPRI）中对涉及异源蛋白-蛋白相互作用的六个目标的对接性能，这些目标的结构已经在轮次进行后公布。我们的总体策略包括使用 ZDOCK 进行蛋白-蛋白对接，使用 IRAD 进行重新排序，以及使用 Rosetta 进行结构细化。此外，我们还广泛使用实验数据来指导我们的对接运行。所有的氨基酸水平的实验信息都被证明是正确的。然而，对于两个目标，我们还使用蛋白质复合物结构作为建模界面的模板。这导致了不正确的预测，可能是由于目标和模板之间的低序列同一性。尽管目标数量较少，但这里描述的性能与我们之前的 CAPRI 报告相比有些不尽如人意，这可能是由于 CAPRI 目标越来越具有挑战性。
