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蛋白质在许多生命进程中起着关键作用﹐通过与其他蛋白质相互作用来发挥其生物学功能。因此﹐研究蛋白质-蛋白质相互作用对于探索生命的真谛﹑理解疾病相关机理﹐以及研究新药提升人们的健康水平具有重要的作用。随着生物信息学的不断发展﹐越来越多的计算方法被应用于蛋白质结构及功能的研究。其中﹐蛋白质-蛋白质对接﹐分子动力学模拟等技术在蛋白质相互作用中得到了较为广泛的应用。本文对蛋白质蛋白质对接及分子动力学模拟等生物信息学方法的基本原理﹐相关软件及其在蛋白质-蛋白质相互作用研究中的应用进行概述。“,”Proteins that play a critical role in many cellular processes often perform their functions by interacting with other proteins. Therefore, the studies of protein-protein interactions are vital to exploring the essence of life, understanding the mechanism of diseases and developing new drugs to improve human health. With the sustained development of bioinformatics, more and more computational methods have been applied to structural and functional research of proteins. Protein-protein docking and molecular dynamics simulation are both widely applied to the studies of protein-protein interactions. This article reviews the theory of computational methods, softwares and the application in protein-protein interactions.