de Vries Sjoerd J, Bonvin Alexandre M J J
Bijvoet Center for Biomolecular Research, Science Faculty, Utrecht University, 3584CH, Utrecht, The Netherlands.
Curr Protein Pept Sci. 2008 Aug;9(4):394-406. doi: 10.2174/138920308785132712.
Protein-protein interface prediction is a booming field, with a substantial growth in the number of new methods being published the last two years. The increasing number of available three-dimensional structures of protein-protein complexes has enabled large-scale statistical analyses of protein interfaces, considering evolutionary, physicochemical and structural properties. Successful combinations of these properties have led to more accurate interface predictors in recent years. In addition to parametric combination, machine learning algorithms have become popular. In the meantime, assessing the absolute and relative performance of interface predictors remains very difficult: This is due to differences in both the output of the various interface predictors, and in the evaluation criteria used by their respective authors. This review provides an overview of the state of the art in the field, and discusses the performance of existing interface predictors. The focus is mainly on protein-protein interface prediction, although most issues are also valid for other kinds of interface prediction.
蛋白质-蛋白质相互作用界面预测是一个蓬勃发展的领域,在过去两年中,新方法的发表数量大幅增长。蛋白质-蛋白质复合物三维结构数量的增加,使得人们能够从进化、物理化学和结构特性等方面对蛋白质界面进行大规模统计分析。近年来,这些特性的成功结合产生了更准确的界面预测方法。除了参数组合外,机器学习算法也变得流行起来。与此同时,评估界面预测方法的绝对和相对性能仍然非常困难:这是由于各种界面预测方法的输出以及各自作者使用的评估标准存在差异。本综述概述了该领域的最新进展,并讨论了现有界面预测方法的性能。尽管大多数问题对于其他类型的界面预测也同样适用,但本文主要关注蛋白质-蛋白质相互作用界面预测。