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An Integrated Approach to Sequence-Independent Local Alignment of Protein Binding Sites

机译：蛋白质结合位点独立于序列的局部比对的综合方法

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摘要

Accurate alignment of protein-protein binding sites can aid in protein docking studies and constructing templates for predicting structure of protein complexes, along with in-depth understanding of evolutionary and functional relationships. However, over the past three decades, structural alignment algorithms have focused predominantly on global alignments with little effort on the alignment of local interfaces. In this paper, we introduce the PBSalign ( rotein-protein inding ite ment) method, which integrates techniques in graph theory, 3D localized shape analysis, geometric scoring, and utilization of physicochemical and geometrical properties. Computational results demonstrate that PBSalign is capable of identifying similar homologous and analogous binding sites accurately and performing alignments with better geometric match measures than existing protein-protein interface comparison tools. The proportion of better alignment quality generated by PBSalign is 46, 56, and 70 percent more than iAlign as judged by the average match index (MI), similarity index (SI), and structural alignment score (SAS), respectively. PBSalign provides the life science community an efficient and accurate solution to binding-site alignment while striking the balance between topological details and computational complexity.
机译：蛋白质-蛋白质结合位点的精确比对可以帮助蛋白质对接研究和构建用于预测蛋白质复合物结构的模板，以及对进化和功能关系的深入了解。然而，在过去的三十年中，结构对齐算法主要集中在全局对齐上，而很少进行本地接口的对齐。在本文中，我们介绍了PBSalign（蛋白质-蛋白质指示法）方法，该方法将图论，3D局部形状分析，几何评分以及理化和几何特性的利用等技术相结合。计算结果表明，PBSalign能够准确识别相似的同源和相似的结合位点，并且比现有的蛋白质-蛋白质界面比较工具具有更好的几何匹配度。根据平均匹配指数（MI），相似性指数（SI）和结构比对得分（SAS）判断，PBSalign产生的比对质量更高的比对质量比iAlign高出46％，56％和70％。 PBSalign为生命科学界提供一种有效且准确的解决方案，以实现结合位点对齐，同时在拓扑细节与计算复杂性之间取得平衡。

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