Amino acid indices and similarity matrices maintained at Kyoto
University. An amino acid index is a set of 20 numerical values
representing any of the different physicochemical and biological
properties of amino acids. The AAindex1 section of the Amino Acid
Index Database is a collection of published indices together with the
result of cluster analysis using the correlation coefficient as the
distance between two indices. This section currently contains 494
indices. Another important feature of amino acids that can be
represented numerically is the similarity between amino acids. Thus, a
similarity matrix, also called a mutation matrix, is a set of 210
numerical values, 20 diagonal and 20x19/2 off-diagonal elements, used
for sequence alignments and similarity searches. The AAindex2 section
of the Amino Acid Index Database is a collection of published amino
acid mutation matrices together with the result of cluster analysis.
This section currently contains 83 matrices.