Performance and enhancement of the LZerD protein assembly pipeline in CAPRI 38‐46

Charles W Christoffer, Genki Terashi, Woong-Hee Shin, Tunde Aderinwale, Sai Raghavendra Maddhuri Venkata Subraman, Lenna X. Peterson, Jacob Verburgt, D. Kihara
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引用次数: 10

Abstract

We report the performance of the protein docking prediction pipeline of our group and the results for Critical Assessment of Prediction of Interactions (CAPRI) rounds 38‐46. The pipeline integrates programs developed in our group as well as other existing scoring functions. The core of the pipeline is the LZerD protein‐protein docking algorithm. If templates of the target complex are not found in PDB, the first step of our docking prediction pipeline is to run LZerD for a query protein pair. Meanwhile, in the case of human group prediction, we survey the literature to find information that can guide the modeling, such as protein‐protein interface information. In addition to any literature information and binding residue prediction, generated docking decoys were selected by a rank aggregation of statistical scoring functions. The top 10 decoys were relaxed by a short molecular dynamics simulation before submission to remove atom clashes and improve side‐chain conformations. In these CAPRI rounds, our group, particularly the LZerD server, showed robust performance. On the other hand, there are failed cases where some other groups were successful. To understand weaknesses of our pipeline, we analyzed sources of errors for failed targets. Since we noted that structure refinement is a step that needs improvement, we newly performed a comparative study of several refinement approaches. Finally, we show several examples that illustrate successful and unsuccessful cases by our group.
CAPRI 38‐46中LZerD蛋白组装管道的性能和增强
我们报告了我们小组蛋白质对接预测管道的性能以及相互作用预测关键评估(CAPRI)第38 - 46轮的结果。该管道集成了我们小组开发的程序以及其他现有的评分功能。该流水线的核心是LZerD蛋白-蛋白对接算法。如果在PDB中没有找到目标复合物的模板,我们对接预测管道的第一步是对查询蛋白对运行LZerD。同时,在人类群体预测的情况下,我们通过查阅文献来寻找可以指导建模的信息,如蛋白质-蛋白质界面信息。除了任何文献信息和结合残基预测外,通过统计评分函数的秩聚合选择生成的对接诱饵。前10名诱饵在提交前进行了短暂的分子动力学模拟,以消除原子冲突并改善侧链构象。在这些CAPRI轮次中,我们的小组,特别是LZerD服务器,表现出了强劲的性能。另一方面,也有一些失败的案例,而其他一些团体成功了。为了了解管道的弱点,我们分析了失败目标的错误来源。由于我们注意到结构细化是一个需要改进的步骤,我们最近对几种细化方法进行了比较研究。最后,我们展示了几个例子,说明了我们小组成功和不成功的案例。
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