Tomii K, Kanehisa M
Institute for Chemical Research, Kyoto University, Japan.
Protein Eng. 1996 Jan;9(1):27-36. doi: 10.1093/protein/9.1.27.
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 20 x 20 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.
氨基酸指数是一组20个数值，代表氨基酸的任何不同物理化学和生化特性。作为之前研究的后续，我们扩大了数据库规模，该数据库目前包含402个已发表的指数，并重新进行了单链聚类分析。结果基本证实了之前的发现。氨基酸的另一个可以用数值表示的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20×20数值。我们收集了42个已发表的矩阵，进行了层次聚类分析，并确定了几个与数据集性质和用于构建突变矩阵的方法相对应的聚类。此外，我们试图通过氨基酸指数的组合来重现每个突变矩阵，以便了解氨基酸的哪些特性得到了最充分的体现。Dayhoff突变矩阵的PAM单位与氨基酸的体积和疏水性之间存在关系。包含402个氨基酸指数和42个氨基酸突变矩阵的数据库在互联网上公开提供。
