AAindex is a comprehensive database that provides numerical indices representing various physicochemical and biochemical properties of amino acids and pairs of amino acids. It consists of two main sections: AAindex1, which contains 434 amino acid indices, and AAindex2, which contains 66 amino acid mutation matrices. Each entry in AAindex1 includes the definition, reference information, related entries with correlation coefficients, and actual data. AAindex2 entries include 210 numerical values for symmetric matrices and 400 or more for non-symmetric matrices. The database can be accessed through the DBGET/LinkDB system at GenomeNet or via anonymous FTP. The AAindex database has been continuously updated and expanded, with contributions from researchers such as Kenta Nakai and Kentaro Tomii.AAindex is a comprehensive database that provides numerical indices representing various physicochemical and biochemical properties of amino acids and pairs of amino acids. It consists of two main sections: AAindex1, which contains 434 amino acid indices, and AAindex2, which contains 66 amino acid mutation matrices. Each entry in AAindex1 includes the definition, reference information, related entries with correlation coefficients, and actual data. AAindex2 entries include 210 numerical values for symmetric matrices and 400 or more for non-symmetric matrices. The database can be accessed through the DBGET/LinkDB system at GenomeNet or via anonymous FTP. The AAindex database has been continuously updated and expanded, with contributions from researchers such as Kenta Nakai and Kentaro Tomii.