The AAindex database is a collection of numerical indices representing various physicochemical and biochemical properties of amino acids and pairs of amino acids. It consists of two sections: AAindex1, containing 434 amino acid indices, and AAindex2, containing 66 amino acid mutation matrices. Each entry in AAindex1 includes an accession number, a short description, reference information, and numerical values for the properties of 20 amino acids. Entries also include neighbor information, linking to other entries with a correlation coefficient of 0.8 or higher. Missing values are estimated using statistical methods. AAindex2 contains symmetric and non-symmetric matrices, with entries containing 210 or more numerical values. The database can be accessed through the DBGET/LinkDB system at GenomeNet or downloaded via anonymous FTP. The database was initiated by Nakai et al., expanded by Tomii and Kanehisa, and is continuously updated. The AAindex database is used to analyze protein sequences and structures, particularly for protein sequence alignments and similarity searches. It is available for retrieval and use, with users required to cite the article when using the database. The database is maintained by the authors and supported by grants from the Japanese Ministry of Education, Science, Sports and Culture. The database includes references to various studies and papers that contributed to its development.The AAindex database is a collection of numerical indices representing various physicochemical and biochemical properties of amino acids and pairs of amino acids. It consists of two sections: AAindex1, containing 434 amino acid indices, and AAindex2, containing 66 amino acid mutation matrices. Each entry in AAindex1 includes an accession number, a short description, reference information, and numerical values for the properties of 20 amino acids. Entries also include neighbor information, linking to other entries with a correlation coefficient of 0.8 or higher. Missing values are estimated using statistical methods. AAindex2 contains symmetric and non-symmetric matrices, with entries containing 210 or more numerical values. The database can be accessed through the DBGET/LinkDB system at GenomeNet or downloaded via anonymous FTP. The database was initiated by Nakai et al., expanded by Tomii and Kanehisa, and is continuously updated. The AAindex database is used to analyze protein sequences and structures, particularly for protein sequence alignments and similarity searches. It is available for retrieval and use, with users required to cite the article when using the database. The database is maintained by the authors and supported by grants from the Japanese Ministry of Education, Science, Sports and Culture. The database includes references to various studies and papers that contributed to its development.