Kamimura M, Takahashi Y
Department of Knowledge-based Information Engineering, Toyohashi University of Technology, Japan.
Comput Appl Biosci. 1994 Apr;10(2):163-9. doi: 10.1093/bioinformatics/10.2.163.
This paper describes phi-psi conformational pattern clustering of protein amino acid residues. The method is based on the potential function method and mode seeking technique. phi-psi conformational pattern distribution maps and their three-dimensional potential surface maps were computed for 20 different kinds of amino acid residues, using 67 proteins (14,723 residues) taken from the Protein Data Bank. It was found that glycine residues of proteins have five major clusters in the phi-psi conformational space, and two or three major clusters were found for the other kinds of residues. Mode seeking on the potential surface of glycine residues identified their representative phi-psi conformational patterns: (82.64 degrees, 9.84 degrees), (-62.63 degrees, -41.71 degrees), (-85.33 degrees, 176.78 degrees), (91.88 degrees, 178.14 degrees) and (167.06 degrees, -175.33 degrees). The details of the method and the results are discussed with new classifications of phi-psi conformational patterns of amino acid residues of proteins.
本文描述了蛋白质氨基酸残基的φ-ψ构象模式聚类。该方法基于势函数法和模式搜索技术。使用从蛋白质数据库中获取的67种蛋白质（14723个残基），计算了20种不同氨基酸残基的φ-ψ构象模式分布图及其三维势面图。研究发现，蛋白质中的甘氨酸残基在φ-ψ构象空间中有五个主要聚类，其他种类的残基有两到三个主要聚类。对甘氨酸残基势面进行模式搜索，确定了它们具有代表性的φ-ψ构象模式：（82.64度，9.84度）、（-62.63度，-41.71度）、（-85.33度，176.78度）、（91.88度，178.14度）和（167.06度，-175.33度）。结合蛋白质氨基酸残基φ-ψ构象模式的新分类，对该方法及结果的细节进行了讨论。
