Fully Blind Docking at the Atomic Level for Protein-Peptide Complex Structure Prediction.
Fully Blind Docking at the Atomic Level for Protein-Peptide Complex Structure Prediction.
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在原子水平上完全盲目对接蛋白质肽复合物结构预测。
DOI：
10.1016/j.str.2016.07.021
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发表时间：
2016-10-04
期刊：
影响因子：
5.7
通讯作者：
Zou, Xiaoqin
中科院分区：
文献类型：
--
作者：
Yan, Chengfei;Xu, Xianjin;Zou, Xiaoqin
蛋白质-肽相互作用在许多细胞过程中起着重要作用。计算机模拟预测蛋白质-肽复合物的结构对于这些过程的机理研究和治疗设计是非常需要的。然而，在不了解肽结合位点和结合肽构象的情况下预测蛋白质-肽复合物的全原子结构仍然是一个巨大的挑战。在这里，我们提出了一种基于对接的方法来预测蛋白质-肽复合物的结构，称为MDockPeP，它从肽序列开始，并将全原子的柔性肽全局对接到蛋白质结构上。在peptiDB基准数据库上使用结合和未结合的蛋白质结构测试MDockPeP。结果显示，MDockPeP分别在95.0%的结合对接情况和92.2%的未结合对接情况中成功地产生近天然肽结合模式。性能明显优于现有的其他对接方法。MDockPeP计算效率高，适合大规模应用。由Yan等人开发的MDockPeP，是一种用于蛋白质-肽复合物结构预测的分子对接方法。MDockPeP从肽序列开始，并将全原子柔性肽全局对接到蛋白质结构上，而不需要关于结合位点的先验知识。
Protein-peptide interactions play an important role in many cellular processes. In silico prediction of protein-peptide complex structure is highly desirable for mechanistic investigation of these processes and for therapeutic design. However, predicting all-atom structures of protein-peptide complexes without any knowledge about the peptide binding site and the bound peptide conformation remains a big challenge. Here, we present a docking-based method for predicting protein-peptide complex structures, referred to as MDockPeP, which starts with the peptide sequence and globally docks the all-atom, flexible peptide onto the protein structure. MDockPeP was tested on the peptiDB benchmarking database, using both bound and unbound protein structures. The results show that MDockPeP successfully generated near-native peptide binding modes in 95.0% of the bound docking cases and in 92.2% of the unbound docking cases, respectively. The performance is significantly better than other existing docking methods. MDockPeP is computationally efficient and suitable for large-scale applications. MDockPeP, developed by Yan et al., is a molecular docking method for protein-peptide complex structure prediction. MDockPeP starts with the peptide sequence and globally docks the all-atom, flexible peptide onto the protein structure with no need for a priori knowledge about the binding site.
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影响因子：
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