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Amino acid exchange tables (also called scoring tables):

List of 71 Amino Acid Matrices in AAindex ver.5.0

copied on September 30, 2002 from http://www.genome.ad.jp/dbget/AAindex/list_of_matrices

ALTS910101 The PAM-120 matrix (Altschul, 1991)
AZAE970101 The single residue substitution matrix from interchanges of spatially neighbouring residues (Azarya-Sprinzak et al., 1997)
AZAE970102 The substitution matrix derived from spatially conserved motifs (Azarya-Sprinzak et al., 1997)
BENS940101 Log-odds scoring matrix collected in 6.4-8.7 PAM (Benner et al., 1994)
BENS940102 Log-odds scoring matrix collected in 22-29 PAM (Benner et al., 1994)
BENS940103 Log-odds scoring matrix collected in 74-100 PAM (Benner et al., 1994)
BENS940104 Genetic code matrix (Benner et al., 1994)
CSEM940101 Residue replace ability matrix (Cserzo et al., 1994)
DAYM780301 Log odds matrix for 250 PAMs (Dayhoff et al., 1978)
FEND850101 Structure-Genetic matrix (Feng et al., 1985)
FITW660101 Mutation values for the interconversion of amino acid pairs (Fitch, 1966)
GEOD900101 Hydrophobicity scoring matrix (George et al., 1990)
GONG920101 The mutation matrix for initially aligning (Gonnet et al., 1992)
GRAR740104 Chemical distance (Grantham, 1974)
HENS920101 BLOSUM45 substitution matrix (Henikoff-Henikoff, 1992)
HENS920102 BLOSUM62 substitution matrix (Henikoff-Henikoff, 1992)
HENS920103 BLOSUM80 substitution matrix (Henikoff-Henikoff, 1992)
JOHM930101 Structure-based amino acid scoring table (Johnson-Overington, 1993)
JOND920103 The 250 PAM PET91 matrix (Jones et al., 1992)
JOND940101 The 250 PAM transmembrane protein exchange matrix (Jones et al., 1994)
KAPO950101 (Kapp et al., 1995)
KOLA920101 Conformational similarity weight matrix (Kolaskar-Kulkarni-Kale, 1992)
KOSJ950101 Context-dependent optimal substitution matrices for exposed helix (Koshi-Goldstein, 1995)
KOSJ950102 Context-dependent optimal substitution matrices for exposed beta (Koshi-Goldstein, 1995)
KOSJ950103 Context-dependent optimal substitution matrices for exposed turn (Koshi-Goldstein, 1995)
KOSJ950104 Context-dependent optimal substitution matrices for exposed coil (Koshi-Goldstein, 1995)
KOSJ950105 Context-dependent optimal substitution matrices for buried helix (Koshi-Goldstein, 1995)
KOSJ950106 Context-dependent optimal substitution matrices for buried beta (Koshi-Goldstein, 1995)
KOSJ950107 Context-dependent optimal substitution matrices for buried turn (Koshi-Goldstein, 1995)
KOSJ950108 Context-dependent optimal substitution matrices for buried coil (Koshi-Goldstein, 1995)
KOSJ950109 Context-dependent optimal substitution matrices for alpha helix (Koshi-Goldstein, 1995)
KOSJ950110 Context-dependent optimal substitution matrices for beta sheet (Koshi-Goldstein, 1995)
KOSJ950111 Context-dependent optimal substitution matrices for turn (Koshi-Goldstein, 1995)
KOSJ950112 Context-dependent optimal substitution matrices for coil (Koshi-Goldstein, 1995)
KOSJ950113 Context-dependent optimal substitution matrices for exposed residues (Koshi-Goldstein, 1995)
KOSJ950114 Context-dependent optimal substitution matrices for buried residues (Koshi-Goldstein, 1995)
KOSJ950115 Context-dependent optimal substitution matrices for all residues (Koshi-Goldstein, 1995)
LEVJ860101 The secondary structure similarity matrix (Levin et al., 1986)
LUTR910101 Structure-based comparison table for outside other class (Luthy et al., 1991)
LUTR910102 Structure-based comparison table for inside other class (Luthy et al., 1991)
LUTR910103 Structure-based comparison table for outside alpha class (Luthy et al., 1991)
LUTR910104 Structure-based comparison table for inside alpha class (Luthy et al., 1991)
LUTR910105 Structure-based comparison table for outside beta class (Luthy et al., 1991)
LUTR910106 Structure-based comparison table for inside beta class (Luthy et al., 1991)
LUTR910107 Structure-based comparison table for other class (Luthy et al., 1991)
LUTR910108 Structure-based comparison table for alpha helix class (Luthy et al., 1991)
LUTR910109 Structure-based comparison table for beta strand class (Luthy et al., 1991)
MCLA710101 The similarity of pairs of amino acids (McLachlan, 1971)
MCLA720101 Chemical similarity scores (McLachlan, 1972)
MEHP950101 (Mehta et al., 1995)
MEHP950102 (Mehta et al., 1995)
MEHP950103 (Mehta et al., 1995)
MIYS930101 Base-substitution-protein-stability matrix (Miyazawa-Jernigan, 1993)
MIYT790101 Amino acid pair distance (Miyata et al., 1979)
MOHR870101 EMPAR matrix (Mohana Rao, 1987)
NIEK910101 Structure-derived correlation matrix 1 (Niefind-Schomburg, 1991)
NIEK910102 Structure-derived correlation matrix 2 (Niefind-Schomburg, 1991)
OVEJ920101 STR matrix from structure-based alignments (Overington et al., 1992)
OVEJ920102 Environment-specific amino acid substitution matrix for alpha residues (Overington et al., 1992)
OVEJ920103 Environment-specific amino acid substitution matrix for beta residues (Overington et al., 1992)
OVEJ920104 Environment-specific amino acid substitution matrix for accessible residues (Overington et al., 1992)
OVEJ920105 Environment-specific amino acid substitution matrix for inaccessible residues (Overington et al., 1992)
QU_C930101 Cross-correlation coefficients of preference factors main chain (Qu et al., 1993)
QU_C930102 Cross-correlation coefficients of preference factors side chain (Qu et al., 1993)
QU_C930103 The mutant distance based on spatial preference factor (Qu et al., 1993)
RIER950101 Hydrophobicity scoring matrix (Riek et al., 1995)
RISJ880101 Scoring matrix (Risler et al., 1988)
TUDE900101 isomorphicity of replacements (Tudos et al., 1990)
VOGG950101 (Vogt et al., 1995)
WEIL970101 WAC matrix constructed from amino acid comparative profiles (Wei et al., 1997)
WEIL970102 Difference matrix obtained by subtracting the BLOSUM62 from the WAC matrix (Wei et al., 1997)