蛋白质结构的验证：非键合原子相互作用模式
Verification of protein structures: patterns of nonbonded atomic interactions.
作者信息
Colovos C, Yeates T O
机构信息
Department of Chemistry & Biochemistry, University of California, Los Angeles 90024-1569.
出版信息
Protein Sci. 1993 Sep;2(9):1511-9. doi: 10.1002/pro.5560020916.
Abstract
A novel method for differentiating between correctly and incorrectly determined regions of protein structures based on characteristic atomic interaction is described. Different types of atoms are distributed nonrandomly with respect to each other in proteins. Errors in model building lead to more randomized distributions of the different atom types, which can be distinguished from correct distributions by statistical methods. Atoms are classified in one of three categories: carbon (C), nitrogen (N), and oxygen (O). This leads to six different combinations of pairwise noncovalently bonded interactions (CC, CN, CO, NN, NO, and OO). A quadratic error function is used to characterize the set of pairwise interactions from nine-residue sliding windows in a database of 96 reliable protein structures. Regions of candidate protein structures that are mistraced or misregistered can then be identified by analysis of the pattern of nonbonded interactions from each window.
摘要
本文描述了一种基于特征原子相互作用区分蛋白质结构中正确和错误确定区域的新方法。在蛋白质中，不同类型的原子彼此之间呈非随机分布。模型构建中的错误会导致不同原子类型的分布更加随机，通过统计方法可以将其与正确分布区分开来。原子分为三类之一：碳（C）、氮（N）和氧（O）。这导致了六种不同的成对非共价键相互作用组合（CC、CN、CO、NN、NO和OO）。使用二次误差函数来表征来自96个可靠蛋白质结构数据库中九个残基滑动窗口的成对相互作用集。然后，通过分析每个窗口中非键相互作用的模式，可以识别候选蛋白质结构中追踪错误或配准错误的区域。
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