Analysis of amino acid indices and mutation matrices for sequence comparison and structure prediction of proteins
Analysis of amino acid indices and mutation matrices for sequence comparison and structure prediction of proteins
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DOI：
10.1093/protein/9.1.27
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发表时间：
1996-01-01
期刊：
影响因子：
--
通讯作者：
Kanehisa, M
中科院分区：
文献类型：
--
作者：
Tomii, K;Kanehisa, M
氨基酸指数是一组20个数值，代表氨基酸的任何不同理化和生化性质，作为前期研究的后续，我们增加了数据库的规模，目前包含402个已发表的指数，并重新进行了单连锁聚类分析，结果基本证实了以前的研究结果，可以用数字表示的氨基酸的另一个重要特征是它们之间的相似性，因此，相似性矩阵，也称为突变矩阵，是一组用于蛋白质序列比对和相似性搜索的20 x20数值，我们收集了42个已发表的矩阵，进行了层次聚类分析，并确定了几个集群对应的性质的数据集和用于构建突变矩阵的方法，此外，我们试图重现每个突变矩阵的氨基酸指数的组合，以了解哪些性质的氨基酸是最反映。Dayhoff突变矩阵的PAM单位与氨基酸的体积和疏水性之间存在一定的关系。
An amino acid index is a set of 20 numerical values representing any of the different physicochemical and biochemical properties of amino acids, As a follow-up to the previous study, we have increased the size of the database, which currently contains 402 published indices, and re-performed the single-linkage cluster analysis, The results basically confirmed the previous findings, Another important feature of amino acids that can be represented numerically is the similarity between them, Thus, a similarity matrix, also called a mutation matrix, is a set of 20x20 numerical values used for protein sequence alignments and similarity searches, We have collected 42 published matrices, performed hierarchical cluster analyses and identified several clusters corresponding to the nature of the data set and the method used for constructing the mutation matrix, Further, we have tried to reproduce each mutation matrix by the combination of amino acid indices in order to understand which properties of amino acids are reflected most. There was a relationship between the PAM units of Dayhoff's mutation matrix and the volume and hydrophobicity of amino acids, The database of 402 amino acid indices and 42 amino acid mutation matrices is made publicly available on the Internet.