| 1. Simple identity, which scores only identical amino acids as a match and all others as a mismatch. |
| 2. Genetic code changes, which score the minimum number of nucleotide changes to change a codon for one amino acid into a
codon for another, due to Fitch (1966), and also with added information based on structural similarity of amino acid side
chains (Feng et al. 1985). A similar matrix based on the assumption that genetic code is the only factor influencing amino
acid substitutions has been produced (Benner et al. 1994).
|
| 3. Matrices based on chemical similarity of amino acid side chains, molecular volume, and polarity and hydrophobicity of amino
acid side chains (see Vogt et al. 1995).
|
| 4. Amino acid substitutions in structurally aligned three-dimensional structures (Risler et al. 1988; matrix JO93, Johnson
and Overington 1993). A similar matrix was described by Henikoff and Henikoff (1993). Sander and Schneider (1991) prepared
a similar matrix based on these same substitutions but augmented by substitutions found in proteins which are so similar to
the structure-solved group that they undoubtedly have the same three-dimensional structure.
|
| 5. Gonnet et al. (1994) have prepared a 400 × 400 dipeptide substitution matrix for aligning proteins based on the possibility
that amino acid substitutions at a particular site are influenced by neighboring amino acids, and thus that the environment
of an amino acid plays a role in protein evolution.
|
| 6. Jones et al. (1994) have prepared a scoring matrix specifically for transmembrane proteins. This matrix was prepared using
an analysis similar to that used for preparing the original Dayhoff PAM matrices, and therefore provides an estimate of evolutionary
distances among members of this class of proteins.
|
