Niefind K, Schomburg D
GBF (Gesellschaft für Biotechnologische Forschung), Department of Molecular Structure Research, Braunschweig, Germany.
J Mol Biol. 1991 Jun 5;219(3):481-97. doi: 10.1016/0022-2836(91)90188-c.
A set of "similarity-parameters" was calculated that reflects the influence of the proteinogenic amino acids on the structure of the protein backbone. The parameters were derived from a detailed analysis of the amino acid specific main-chain torsion angle distributions as they are found in proteins (highly resolved protein structures from the Brookhaven Protein Data Bank). The purpose of these parameters is threefold: (1) they should help in estimating the structural effect of an amino acid substitution during the design of new mutants in protein-engineering; (2) in modeling by homology they should mark places in the protein where changes in the folding are expected; and (3) they should form a scoring matrix in protein sequence alignment superior to identity scoring. The usability of the "structure derived correlation matrix (SCM)" for these purposes is assessed and demonstrated for some examples in the paper.
计算出了一组“相似性参数”，该参数反映了蛋白质ogenic氨基酸对蛋白质主链结构的影响。这些参数源自对蛋白质中氨基酸特异性主链扭转角分布的详细分析（来自布鲁克海文蛋白质数据库的高分辨率蛋白质结构）。这些参数的目的有三个：（1）在蛋白质工程中设计新突变体时，它们应有助于估计氨基酸取代的结构效应；（2）在同源建模中，它们应标记出蛋白质中预期折叠会发生变化的位置；（3）它们应在蛋白质序列比对中形成一个优于同一性评分的评分矩阵。本文通过一些示例评估并展示了“结构衍生相关矩阵（SCM）”用于这些目的的可用性。
