Given the importance of peptide-mediated protein interactions in cellular processes, protein–peptide docking has received increasing attention. Here, we have developed a Hierarchical flexible Peptide Docking approach through fast generation and ensemble docking of peptide conformations, which is referred to as HPepDock. Tested on the LEADS-PEP benchmark data set of 53 diverse complexes with peptides of 3–12 residues, HPepDock performed significantly better than the 11 docking protocols of five small-molecule docking programs (DOCK, AutoDock, AutoDock Vina, Surflex, and GOLD) in predicting near-native binding conformations. HPepDock was also evaluated on the 19 bound/unbound and 10 unbound/unbound protein–peptide complexes of the Glide SP-PEP benchmark and showed an overall better performance than Glide SP-PEP+MM-GBSA and FlexPepDock in both bound and unbound docking. HPepDock is computationally efficient, and the average running time for docking a peptide is ∼15 min with the range from about 1 min for short peptides to around 40 min for long peptides.

中文翻译：

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通过构象异构体生成和多肽的整体对接进行的分层柔性肽对接

考虑到肽介导的蛋白质相互作用在细胞过程中的重要性，蛋白质-肽对接受到越来越多的关注。在这里，我们已经开发出一种ħ ierarchical柔性打气潮基座荷兰国际集团通过快速产生和肽构象的对接合奏方法，其被称为HPepDock。在53种具有3-12个残基的肽的复合物的LEADS-PEP基准数据集上进行测试，HPepDock的性能明显优于五个小分子对接程序（DOCK，AutoDock，AutoDock Vina，Surflex和GOLD）的11个对接方案在预测近天然结合构象中。HPepDock还对Glide SP-PEP基准测试的19种结合/未结合和10种未结合/未结合的蛋白-肽复合物进行了评估，在结合和未结合对接方面均显示出比Glide SP-PEP + MM-GBSA和FlexPepDock更好的整体性能。HPepDock计算效率高，对接肽的平均运行时间约为15分钟，范围从短肽约1分钟到长肽约40分钟。