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首页> 外文期刊>IEEE/ACM transactions on computational biology and bioinformatics >SP-Dock: Protein-Protein Docking Using Shape and Physicochemical Complementarity
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SP-Dock: Protein-Protein Docking Using Shape and Physicochemical Complementarity

机译：SP-Dock：利用形状和物理化学互补性进行蛋白质-蛋白质对接

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摘要

In this paper, a framework for protein-protein docking is proposed, which exploits both shape and physicochemical complementarity to generate improved docking predictions. Shape complementarity is achieved by matching local surface patches. However, unlike existing approaches, which are based on single-patch or two-patch matching, we developed a new algorithm that compares simultaneously, groups of neighboring patches from the receptor with groups of neighboring patches from the ligand. Taking into account the fact that shape complementarity in protein surfaces is mostly approximate rather than exact, the proposed group-based matching algorithm fits perfectly to the nature of protein surfaces. This is demonstrated by the high performance that our method achieves especially in the case where the unbound structures of the proteins are considered. Additionally, several physicochemical factors, such as desolvation energy, electrostatic complementarity (EC), hydrophobicity (HP), Coulomb potential (CP), and Lennard-Jones potential are integrated using an optimized scoring function, improving geometric ranking in more than 60 percent of the complexes of Docking Benchmark 2.4.
机译：本文提出了蛋白质-蛋白质对接的框架，该框架利用形状和物理化学互补性来产生改进的对接预测。形状互补是通过匹配局部表面斑块来实现的。但是，与基于单补丁或两补丁匹配的现有方法不同，我们开发了一种新算法，该算法可以同时比较来自受体的相邻补丁组和来自配体的相邻补丁组。考虑到蛋白质表面的形状互补性大多是近似而非精确的事实，因此，基于组的匹配算法非常适合蛋白质表面的性质。我们的方法获得的高性能证明了这一点，特别是在考虑蛋白质的未结合结构的情况下。此外，使用优化的评分功能将去溶剂化能量，静电互补性（EC），疏水性（HP），库仑势（CP）和Lennard-Jones势等几种物理化学因素进行了积分，从而将几何排名提高了60％以上Docking Benchmark 2.4的复杂性。

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