ANALYSIS OF AMINO-ACID INDEXES AND MUTATION MATRICES FOR SEQUENCE COMPARISON AND STRUCTURE PREDICTION OF PROTEINS

An amino acid index is a set of 20 numerical values representing any o f the different physicochemical and biochemical properties of amino ac ids, As a follow-up to the previous study, we have increased the size of the database, which currently contains 402 published indices, and r e-performed the single-linkage cluster analysis, The results basically confirmed the previous findings, Another important feature of amino a cids that can be represented numerically is the similarity between the m, Thus, a similarity matrix, also called a mutation matrix, is a set of 20x20 numerical values used for protein sequence alignments and sim ilarity searches, We have collected 42 published matrices, performed h ierarchical cluster analyses and identified several clusters correspon ding to the nature of the data set and the method used for constructin g the mutation matrix, Further, we have tried to reproduce each mutati on matrix by the combination of amino acid indices in order to underst and which properties of amino acids are reflected most. There was a re lationship between the PAM units of Dayhoff's mutation matrix and the volume and hydrophobicity of amino acids, The database of 402 amino ac id indices and 42 amino acid mutation matrices is made publicly availa ble on the Internet.