Interolog interfaces in protein-protein docking.
Interolog interfaces in protein-protein docking.
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DOI：
10.1002/prot.24788
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发表时间：
2015-11
影响因子：
2.9
通讯作者：
Mitchell, Julie C.
中科院分区：
文献类型：
--
作者：
Alsop, James D.;Mitchell, Julie C.
蛋白质是生物系统的基本元素，它们的功能通常依赖于它们成功结合特定伴侣的能力。近年来，蛋白质相互作用的研究重点集中在结合界面中对结合能学有重要贡献的残基。在本研究中，我们探讨了如何利用热点守恒来指导对接预测。我们表明，将进化数据与热点预测相结合，在一系列基准示例中突出了近原生结构。我们的方法探索了使用热点和进化数据对蛋白质复合物进行评分的各种策略，使用绝对和化学守恒定义以及对这些策略的改进，这些策略着眼于窗口守恒和过滤，以确保每个结合伙伴中热点的最小数量。最后，生成基于结构的同源物模型，与基于序列的评分进行比较。使用22个和85个示例的两个数据集，观察到前10名和前1名的预测率很高，根据所应用的数据集和策略，高达82%的示例返回前10名，35%返回前1名；在诱饵中包含原生结构后，高达55%的示例产生了前1命中。数据集之间的20个常见示例表明，更精心策划的内部数据可以产生更好的预测，特别是在获得前1个命中值方面。蛋白质2015;83:1940 - 1946。©2015作者。蛋白质：结构、功能和生物信息学出版于Wiley期刊公司。
Proteins are essential elements of biological systems, and their function typically relies on their ability to successfully bind to specific partners. Recently, an emphasis of study into protein interactions has been on hot spots, or residues in the binding interface that make a significant contribution to the binding energetics. In this study, we investigate how conservation of hot spots can be used to guide docking prediction. We show that the use of evolutionary data combined with hot spot prediction highlights near‐native structures across a range of benchmark examples. Our approach explores various strategies for using hot spots and evolutionary data to score protein complexes, using both absolute and chemical definitions of conservation along with refinements to these strategies that look at windowed conservation and filtering to ensure a minimum number of hot spots in each binding partner. Finally, structure‐based models of orthologs were generated for comparison with sequence‐based scoring. Using two data sets of 22 and 85 examples, a high rate of top 10 and top 1 predictions are observed, with up to 82% of examples returning a top 10 hit and 35% returning top 1 hit depending on the data set and strategy applied; upon inclusion of the native structure among the decoys, up to 55% of examples yielded a top 1 hit. The 20 common examples between data sets show that more carefully curated interolog data yields better predictions, particularly in achieving top 1 hits. Proteins 2015; 83:1940–1946. © 2015 The Authors. Proteins: Structure, Function, and Bioinformatics Published by Wiley Periodicals, Inc.
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