Supplemental information for "Use of the codon table to quantify the evolutionary role of random mutations" by Mihaly Mezei Correlations with unweighted single mutant paths ALTS910101 The PAM-120 matrix (Altschul, 1991) Correlation with mutation matrix= 0.508 (all elements) 0.389 (Only nonzero elements) BENS940101 Log-odds scoring matrix collected in 6.4-8.7 PAM (Benner et al., 1994) Correlation with mutation matrix= 0.488 (all elements) 0.306 (Only nonzero elements) BENS940102 Log-odds scoring matrix collected in 22-29 PAM (Benner et al., 1994) Correlation with mutation matrix= 0.469 (all elements) 0.333 (Only nonzero elements) BENS940103 Log-odds scoring matrix collected in 74-100 PAM (Benner et al., 1994) Correlation with mutation matrix= 0.447 (all elements) 0.363 (Only nonzero elements) BENS940104 Genetic code matrix (Benner et al., 1994) Correlation with mutation matrix= 0.570 (all elements) 0.286 (Only nonzero elements) CSEM940101 Residue replace ability matrix (Cserzo et al., 1994) Correlation with mutation matrix= 0.542 (all elements) 0.484 (Only nonzero elements) DAYM780301 Log odds matrix for 250 PAMs (Dayhoff et al., 1978) Correlation with mutation matrix= 0.449 (all elements) 0.338 (Only nonzero elements) FEND850101 Structure-Genetic matrix (Feng et al., 1985) Correlation with mutation matrix= 0.627 (all elements) 0.491 (Only nonzero elements) FITW660101 Mutation values for the interconversion of amino acid pairs (Fitch, 1966) Correlation with mutation matrix= -0.649 (all elements) -0.545 (Only nonzero elements) GEOD900101 Hydrophobicity scoring matrix (George et al., 1990) Correlation with mutation matrix= 0.291 (all elements) 0.364 (Only nonzero elements) GONG920101 The mutation matrix for initially aligning (Gonnet et al., 1992) Correlation with mutation matrix= 0.441 (all elements) 0.371 (Only nonzero elements) GRAR740104 Chemical distance (Grantham, 1974) Correlation with mutation matrix= -0.426 (all elements) -0.400 (Only nonzero elements) HENS920101 BLOSUM45 substitution matrix (Henikoff-Henikoff, 1992) Correlation with mutation matrix= 0.487 (all elements) 0.429 (Only nonzero elements) HENS920102 BLOSUM62 substitution matrix (Henikoff-Henikoff, 1992) Correlation with mutation matrix= 0.506 (all elements) 0.439 (Only nonzero elements) HENS920103 BLOSUM80 substitution matrix (Henikoff-Henikoff, 1992) Correlation with mutation matrix= 0.521 (all elements) 0.447 (Only nonzero elements) JOHM930101 Structure-based amino acid scoring table (Johnson-Overington, 1993) Correlation with mutation matrix= 0.503 (all elements) 0.430 (Only nonzero elements) JOND920103 The 250 PAM PET91 matrix (Jones et al., 1992) Correlation with mutation matrix= 0.476 (all elements) 0.318 (Only nonzero elements) JOND940101 The 250 PAM transmembrane protein exchange matrix (Jones et al., 1994) Correlation with mutation matrix= 0.404 (all elements) 0.169 (Only nonzero elements) KOLA920101 Conformational similarity weight matrix (Kolaskar-Kulkarni-Kale, 1992) Correlation with mutation matrix= 0.390 (all elements) 0.327 (Only nonzero elements) LEVJ860101 The secondary structure similarity matrix (Levin et al., 1986) Correlation with mutation matrix= 0.539 (all elements) 0.490 (Only nonzero elements) LUTR910101 Structure-based comparison table for outside other class (Luthy et al., 1991) Correlation with mutation matrix= 0.404 (all elements) 0.351 (Only nonzero elements) LUTR910102 Structure-based comparison table for inside other class (Luthy et al., 1991) Correlation with mutation matrix= 0.374 (all elements) 0.384 (Only nonzero elements) LUTR910103 Structure-based comparison table for outside alpha class (Luthy et al., 1991) Correlation with mutation matrix= 0.350 (all elements) 0.368 (Only nonzero elements) LUTR910104 Structure-based comparison table for inside alpha class (Luthy et al., 1991) Correlation with mutation matrix= 0.320 (all elements) 0.277 (Only nonzero elements) LUTR910105 Structure-based comparison table for outside beta class (Luthy et al., 1991) Correlation with mutation matrix= 0.388 (all elements) 0.332 (Only nonzero elements) LUTR910106 Structure-based comparison table for inside beta class (Luthy et al., 1991) Correlation with mutation matrix= 0.393 (all elements) 0.384 (Only nonzero elements) LUTR910107 Structure-based comparison table for other class (Luthy et al., 1991) Correlation with mutation matrix= 0.405 (all elements) 0.366 (Only nonzero elements) LUTR910108 Structure-based comparison table for alpha helix class (Luthy et al., 1991) Correlation with mutation matrix= 0.353 (all elements) 0.359 (Only nonzero elements) LUTR910109 Structure-based comparison table for beta strand class (Luthy et al., 1991) Correlation with mutation matrix= 0.422 (all elements) 0.400 (Only nonzero elements) MCLA710101 The similarity of pairs of amino acids (McLachlan, 1971) Correlation with mutation matrix= 0.559 (all elements) 0.502 (Only nonzero elements) MCLA720101 Chemical similarity scores (McLachlan, 1972) Correlation with mutation matrix= 0.583 (all elements) 0.524 (Only nonzero elements) MIYS930101 Base-substitution-protein-stability matrix (Miyazawa-Jernigan, 1993) Correlation with mutation matrix= 0.479 (all elements) 0.357 (Only nonzero elements) MIYT790101 Amino acid pair distance (Miyata et al., 1979) Correlation with mutation matrix= -0.451 (all elements) -0.413 (Only nonzero elements) MOHR870101 EMPAR matrix (Mohana Rao, 1987) Correlation with mutation matrix= 0.461 (all elements) 0.475 (Only nonzero elements) NIEK910101 Structure-derived correlation matrix 1 (Niefind-Schomburg, 1991) Correlation with mutation matrix= 0.499 (all elements) 0.468 (Only nonzero elements) NIEK910102 Structure-derived correlation matrix 2 (Niefind-Schomburg, 1991) Correlation with mutation matrix= 0.484 (all elements) 0.452 (Only nonzero elements) OVEJ920101 STR matrix from structure-based alignments (Overington et al., 1992) Correlation with mutation matrix= 0.503 (all elements) 0.437 (Only nonzero elements) QU_C930101 Cross-correlation coefficients of preference factors Correlation with mutation matrix= 0.403 (all elements) 0.475 (Only nonzero elements) QU_C930102 Cross-correlation coefficients of preference factors Correlation with mutation matrix= 0.329 (all elements) 0.345 (Only nonzero elements) QU_C930103 The mutant distance based on spatial preference factor (Qu et al., 1993) Correlation with mutation matrix= 0.462 (all elements) 0.499 (Only nonzero elements) RISJ880101 Scoring matrix (Risler et al., 1988) Correlation with mutation matrix= 0.394 (all elements) 0.354 (Only nonzero elements) TUDE900101 isomorphicity of replacements (Tudos et al., 1990) Correlation with mutation matrix= 0.587 (all elements) 0.537 (Only nonzero elements) AZAE970101 The single residue substitution matrix from interchanges of Correlation with mutation matrix= 0.245 (all elements) 0.341 (Only nonzero elements) AZAE970102 The substitution matrix derived from spatially conserved motifs Correlation with mutation matrix= 0.254 (all elements) 0.334 (Only nonzero elements) RIER950101 Hydrophobicity scoring matrix (Riek et al., 1995) Correlation with mutation matrix= 0.135 (all elements) 0.250 (Only nonzero elements) WEIL970101 WAC matrix constructed from amino acid comparative profiles (Wei et al., 1997) Correlation with mutation matrix= 0.414 (all elements) 0.483 (Only nonzero elements) WEIL970102 Difference matrix obtained by subtracting the BLOSUM62 from the WAC Correlation with mutation matrix= -0.273 (all elements) -0.325 (Only nonzero elements) MEHP950101 (Mehta et al., 1995) Correlation with mutation matrix= 0.006 (all elements) -0.015 (Only nonzero elements) MEHP950102 (Mehta et al., 1995) Correlation with mutation matrix= -0.026 (all elements) -0.029 (Only nonzero elements) MEHP950103 (Mehta et al., 1995) Correlation with mutation matrix= 0.049 (all elements) 0.077 (Only nonzero elements) KAPO950101 (Kapp et al., 1995) Correlation with mutation matrix= 0.329 (all elements) 0.206 (Only nonzero elements) VOGG950101 (Vogt et al., 1995) Correlation with mutation matrix= 0.441 (all elements) 0.371 (Only nonzero elements) KOSJ950101 Context-dependent optimal substitution matrices for exposed helix Correlation with mutation matrix= 0.045 (all elements) -0.024 (Only nonzero elements) KOSJ950102 Context-dependent optimal substitution matrices for exposed beta Correlation with mutation matrix= 0.074 (all elements) 0.072 (Only nonzero elements) KOSJ950103 Context-dependent optimal substitution matrices for exposed turn Correlation with mutation matrix= 0.063 (all elements) 0.013 (Only nonzero elements) KOSJ950104 Context-dependent optimal substitution matrices for exposed coil Correlation with mutation matrix= 0.038 (all elements) -0.028 (Only nonzero elements) KOSJ950105 Context-dependent optimal substitution matrices for buried helix Correlation with mutation matrix= 0.022 (all elements) 0.008 (Only nonzero elements) KOSJ950106 Context-dependent optimal substitution matrices for buried beta Correlation with mutation matrix= 0.020 (all elements) -0.008 (Only nonzero elements) KOSJ950107 Context-dependent optimal substitution matrices for buried turn Correlation with mutation matrix= 0.058 (all elements) 0.056 (Only nonzero elements) KOSJ950108 Context-dependent optimal substitution matrices for buried coil Correlation with mutation matrix= 0.030 (all elements) 0.021 (Only nonzero elements) KOSJ950109 Context-dependent optimal substitution matrices for alpha helix Correlation with mutation matrix= 0.043 (all elements) 0.023 (Only nonzero elements) KOSJ950110 Context-dependent optimal substitution matrices for beta sheet Correlation with mutation matrix= 0.045 (all elements) 0.028 (Only nonzero elements) KOSJ950111 Context-dependent optimal substitution matrices for turn Correlation with mutation matrix= 0.059 (all elements) 0.031 (Only nonzero elements) KOSJ950112 Context-dependent optimal substitution matrices for coil Correlation with mutation matrix= 0.039 (all elements) 0.000 (Only nonzero elements) KOSJ950113 Context-dependent optimal substitution matrices for exposed residues Correlation with mutation matrix= 0.049 (all elements) 0.003 (Only nonzero elements) KOSJ950114 Context-dependent optimal substitution matrices for buried residues Correlation with mutation matrix= 0.040 (all elements) 0.042 (Only nonzero elements) KOSJ950115 Context-dependent optimal substitution matrices for all residues Correlation with mutation matrix= 0.048 (all elements) 0.025 (Only nonzero elements) OVEJ920102 Environment-specific amino acid substitution matrix for alpha residues Correlation with mutation matrix= 0.524 (all elements) 0.347 (Only nonzero elements) OVEJ920103 Environment-specific amino acid substitution matrix for beta residues Correlation with mutation matrix= 0.559 (all elements) 0.373 (Only nonzero elements) OVEJ920104 Environment-specific amino acid substitution matrix for accessible Correlation with mutation matrix= 0.550 (all elements) 0.367 (Only nonzero elements) OVEJ920105 Environment-specific amino acid substitution matrix for inaccessible residues Correlation with mutation matrix= 0.574 (all elements) 0.404 (Only nonzero elements) LINK010101 Substitution matrices from an neural network model (Lin et al., 2001) Correlation with mutation matrix= 0.595 (all elements) 0.508 (Only nonzero elements) BLAJ010101 Matrix built from structural superposition data for identifying potential Correlation with mutation matrix= 0.399 (all elements) 0.301 (Only nonzero elements) PRLA000101 Structure derived matrix (SDM) for alignment of distantly related sequences Correlation with mutation matrix= 0.436 (all elements) 0.369 (Only nonzero elements) PRLA000102 Homologous structure dereived matrix (HSDM) for alignment of distantly Correlation with mutation matrix= 0.440 (all elements) 0.372 (Only nonzero elements) DOSZ010101 Amino acid similarity matrix based on the sausage force Correlation with mutation matrix= 0.147 (all elements) 0.006 (Only nonzero elements) DOSZ010102 Normalised version of SM_SAUSAGE (Dosztanyi-Torda, 2001) Correlation with mutation matrix= 0.418 (all elements) 0.368 (Only nonzero elements) DOSZ010103 An amino acid similarity matrix based on the THREADER force field Correlation with mutation matrix= 0.441 (all elements) 0.364 (Only nonzero elements) DOSZ010104 Normalised version of SM_THREADER (Dosztanyi-Torda, 2001) Correlation with mutation matrix= 0.489 (all elements) 0.397 (Only nonzero elements) GIAG010101 Residue substitutions matrix from thermo/mesophilic to psychrophilic Correlation with mutation matrix= -0.010 (all elements) -0.005 (Only nonzero elements) DAYM780302 Log odds matrix for 40 PAMs (Dayhoff et al., 1978) Correlation with mutation matrix= 0.562 (all elements) 0.481 (Only nonzero elements) HENS920104 BLOSUM50 substitution matrix (Henikoff-Henikoff, 1992) Correlation with mutation matrix= 0.483 (all elements) 0.413 (Only nonzero elements) QUIB020101 STROMA score matrix for the alignment of known distant homologs Correlation with mutation matrix= 0.429 (all elements) 0.348 (Only nonzero elements) Correlations single mutant paths weighted with human codon usage frequencies ALTS910101 The PAM-120 matrix (Altschul, 1991) Correlation with mutation matrix= 0.540 (all elements) 0.364 (Only nonzero elements) BENS940101 Log-odds scoring matrix collected in 6.4-8.7 PAM (Benner et al., 1994) Correlation with mutation matrix= 0.626 (all elements) 0.507 (Only nonzero elements) BENS940102 Log-odds scoring matrix collected in 22-29 PAM (Benner et al., 1994) Correlation with mutation matrix= 0.577 (all elements) 0.486 (Only nonzero elements) BENS940103 Log-odds scoring matrix collected in 74-100 PAM (Benner et al., 1994) Correlation with mutation matrix= 0.518 (all elements) 0.462 (Only nonzero elements) BENS940104 Genetic code matrix (Benner et al., 1994) Correlation with mutation matrix= 0.802 (all elements) 0.713 (Only nonzero elements) CSEM940101 Residue replace ability matrix (Cserzo et al., 1994) Correlation with mutation matrix= 0.545 (all elements) 0.467 (Only nonzero elements) DAYM780301 Log odds matrix for 250 PAMs (Dayhoff et al., 1978) Correlation with mutation matrix= 0.480 (all elements) 0.326 (Only nonzero elements) FEND850101 Structure-Genetic matrix (Feng et al., 1985) Correlation with mutation matrix= 0.652 (all elements) 0.387 (Only nonzero elements) FITW660101 Mutation values for the interconversion of amino acid pairs (Fitch, 1966) Correlation with mutation matrix= -0.709 (all elements) -0.411 (Only nonzero elements) GEOD900101 Hydrophobicity scoring matrix (George et al., 1990) Correlation with mutation matrix= 0.284 (all elements) 0.364 (Only nonzero elements) GONG920101 The mutation matrix for initially aligning (Gonnet et al., 1992) Correlation with mutation matrix= 0.503 (all elements) 0.458 (Only nonzero elements) GRAR740104 Chemical distance (Grantham, 1974) Correlation with mutation matrix= -0.380 (all elements) -0.279 (Only nonzero elements) HENS920101 BLOSUM45 substitution matrix (Henikoff-Henikoff, 1992) Correlation with mutation matrix= 0.491 (all elements) 0.420 (Only nonzero elements) HENS920102 BLOSUM62 substitution matrix (Henikoff-Henikoff, 1992) Correlation with mutation matrix= 0.518 (all elements) 0.440 (Only nonzero elements) HENS920103 BLOSUM80 substitution matrix (Henikoff-Henikoff, 1992) Correlation with mutation matrix= 0.532 (all elements) 0.441 (Only nonzero elements) JOHM930101 Structure-based amino acid scoring table (Johnson-Overington, 1993) Correlation with mutation matrix= 0.507 (all elements) 0.400 (Only nonzero elements) JOND920103 The 250 PAM PET91 matrix (Jones et al., 1992) Correlation with mutation matrix= 0.596 (all elements) 0.486 (Only nonzero elements) JOND940101 The 250 PAM transmembrane protein exchange matrix (Jones et al., 1994) Correlation with mutation matrix= 0.591 (all elements) 0.444 (Only nonzero elements) KOLA920101 Conformational similarity weight matrix (Kolaskar-Kulkarni-Kale, 1992) Correlation with mutation matrix= 0.384 (all elements) 0.282 (Only nonzero elements) LEVJ860101 The secondary structure similarity matrix (Levin et al., 1986) Correlation with mutation matrix= 0.515 (all elements) 0.439 (Only nonzero elements) LUTR910101 Structure-based comparison table for outside other class (Luthy et al., 1991) Correlation with mutation matrix= 0.422 (all elements) 0.365 (Only nonzero elements) LUTR910102 Structure-based comparison table for inside other class (Luthy et al., 1991) Correlation with mutation matrix= 0.389 (all elements) 0.411 (Only nonzero elements) LUTR910103 Structure-based comparison table for outside alpha class (Luthy et al., 1991) Correlation with mutation matrix= 0.365 (all elements) 0.394 (Only nonzero elements) LUTR910104 Structure-based comparison table for inside alpha class (Luthy et al., 1991) Correlation with mutation matrix= 0.340 (all elements) 0.290 (Only nonzero elements) LUTR910105 Structure-based comparison table for outside beta class (Luthy et al., 1991) Correlation with mutation matrix= 0.397 (all elements) 0.321 (Only nonzero elements) LUTR910106 Structure-based comparison table for inside beta class (Luthy et al., 1991) Correlation with mutation matrix= 0.364 (all elements) 0.327 (Only nonzero elements) LUTR910107 Structure-based comparison table for other class (Luthy et al., 1991) Correlation with mutation matrix= 0.426 (all elements) 0.389 (Only nonzero elements) LUTR910108 Structure-based comparison table for alpha helix class (Luthy et al., 1991) Correlation with mutation matrix= 0.376 (all elements) 0.396 (Only nonzero elements) LUTR910109 Structure-based comparison table for beta strand class (Luthy et al., 1991) Correlation with mutation matrix= 0.393 (all elements) 0.329 (Only nonzero elements) MCLA710101 The similarity of pairs of amino acids (McLachlan, 1971) Correlation with mutation matrix= 0.541 (all elements) 0.427 (Only nonzero elements) MCLA720101 Chemical similarity scores (McLachlan, 1972) Correlation with mutation matrix= 0.540 (all elements) 0.447 (Only nonzero elements) MIYS930101 Base-substitution-protein-stability matrix (Miyazawa-Jernigan, 1993) Correlation with mutation matrix= 0.607 (all elements) 0.567 (Only nonzero elements) MIYT790101 Amino acid pair distance (Miyata et al., 1979) Correlation with mutation matrix= -0.452 (all elements) -0.383 (Only nonzero elements) MOHR870101 EMPAR matrix (Mohana Rao, 1987) Correlation with mutation matrix= 0.455 (all elements) 0.477 (Only nonzero elements) NIEK910101 Structure-derived correlation matrix 1 (Niefind-Schomburg, 1991) Correlation with mutation matrix= 0.474 (all elements) 0.420 (Only nonzero elements) NIEK910102 Structure-derived correlation matrix 2 (Niefind-Schomburg, 1991) Correlation with mutation matrix= 0.470 (all elements) 0.419 (Only nonzero elements) OVEJ920101 STR matrix from structure-based alignments (Overington et al., 1992) Correlation with mutation matrix= 0.508 (all elements) 0.407 (Only nonzero elements) QU_C930101 Cross-correlation coefficients of preference factors Correlation with mutation matrix= 0.329 (all elements) 0.402 (Only nonzero elements) QU_C930102 Cross-correlation coefficients of preference factors Correlation with mutation matrix= 0.355 (all elements) 0.405 (Only nonzero elements) QU_C930103 The mutant distance based on spatial preference factor (Qu et al., 1993) Correlation with mutation matrix= 0.431 (all elements) 0.474 (Only nonzero elements) RISJ880101 Scoring matrix (Risler et al., 1988) Correlation with mutation matrix= 0.285 (all elements) 0.057 (Only nonzero elements) TUDE900101 isomorphicity of replacements (Tudos et al., 1990) Correlation with mutation matrix= 0.537 (all elements) 0.448 (Only nonzero elements) AZAE970101 The single residue substitution matrix from interchanges of Correlation with mutation matrix= 0.184 (all elements) 0.243 (Only nonzero elements) AZAE970102 The substitution matrix derived from spatially conserved motifs Correlation with mutation matrix= 0.202 (all elements) 0.251 (Only nonzero elements) RIER950101 Hydrophobicity scoring matrix (Riek et al., 1995) Correlation with mutation matrix= 0.135 (all elements) 0.310 (Only nonzero elements) WEIL970101 WAC matrix constructed from amino acid comparative profiles (Wei et al., 1997) Correlation with mutation matrix= 0.346 (all elements) 0.413 (Only nonzero elements) WEIL970102 Difference matrix obtained by subtracting the BLOSUM62 from the WAC Correlation with mutation matrix= -0.145 (all elements) -0.071 (Only nonzero elements) MEHP950101 (Mehta et al., 1995) Correlation with mutation matrix= 0.089 (all elements) 0.202 (Only nonzero elements) MEHP950102 (Mehta et al., 1995) Correlation with mutation matrix= -0.070 (all elements) -0.131 (Only nonzero elements) MEHP950103 (Mehta et al., 1995) Correlation with mutation matrix= -0.013 (all elements) -0.056 (Only nonzero elements) KAPO950101 (Kapp et al., 1995) Correlation with mutation matrix= 0.387 (all elements) 0.270 (Only nonzero elements) VOGG950101 (Vogt et al., 1995) Correlation with mutation matrix= 0.503 (all elements) 0.458 (Only nonzero elements) KOSJ950101 Context-dependent optimal substitution matrices for exposed helix Correlation with mutation matrix= 0.098 (all elements) 0.046 (Only nonzero elements) KOSJ950102 Context-dependent optimal substitution matrices for exposed beta Correlation with mutation matrix= 0.086 (all elements) 0.095 (Only nonzero elements) KOSJ950103 Context-dependent optimal substitution matrices for exposed turn Correlation with mutation matrix= 0.111 (all elements) 0.087 (Only nonzero elements) KOSJ950104 Context-dependent optimal substitution matrices for exposed coil Correlation with mutation matrix= 0.096 (all elements) 0.058 (Only nonzero elements) KOSJ950105 Context-dependent optimal substitution matrices for buried helix Correlation with mutation matrix= 0.058 (all elements) 0.082 (Only nonzero elements) KOSJ950106 Context-dependent optimal substitution matrices for buried beta Correlation with mutation matrix= 0.066 (all elements) 0.082 (Only nonzero elements) KOSJ950107 Context-dependent optimal substitution matrices for buried turn Correlation with mutation matrix= 0.089 (all elements) 0.124 (Only nonzero elements) KOSJ950108 Context-dependent optimal substitution matrices for buried coil Correlation with mutation matrix= 0.069 (all elements) 0.103 (Only nonzero elements) KOSJ950109 Context-dependent optimal substitution matrices for alpha helix Correlation with mutation matrix= 0.077 (all elements) 0.086 (Only nonzero elements) KOSJ950110 Context-dependent optimal substitution matrices for beta sheet Correlation with mutation matrix= 0.076 (all elements) 0.087 (Only nonzero elements) KOSJ950111 Context-dependent optimal substitution matrices for turn Correlation with mutation matrix= 0.098 (all elements) 0.100 (Only nonzero elements) KOSJ950112 Context-dependent optimal substitution matrices for coil Correlation with mutation matrix= 0.083 (all elements) 0.077 (Only nonzero elements) KOSJ950113 Context-dependent optimal substitution matrices for exposed residues Correlation with mutation matrix= 0.097 (all elements) 0.082 (Only nonzero elements) KOSJ950114 Context-dependent optimal substitution matrices for buried residues Correlation with mutation matrix= 0.068 (all elements) 0.105 (Only nonzero elements) KOSJ950115 Context-dependent optimal substitution matrices for all residues Correlation with mutation matrix= 0.085 (all elements) 0.093 (Only nonzero elements) OVEJ920102 Environment-specific amino acid substitution matrix for alpha residues Correlation with mutation matrix= 0.438 (all elements) 0.443 (Only nonzero elements) OVEJ920103 Environment-specific amino acid substitution matrix for beta residues Correlation with mutation matrix= 0.457 (all elements) 0.423 (Only nonzero elements) OVEJ920104 Environment-specific amino acid substitution matrix for accessible Correlation with mutation matrix= 0.457 (all elements) 0.431 (Only nonzero elements) OVEJ920105 Environment-specific amino acid substitution matrix for inaccessible residues Correlation with mutation matrix= 0.458 (all elements) 0.435 (Only nonzero elements) LINK010101 Substitution matrices from an neural network model (Lin et al., 2001) Correlation with mutation matrix= 0.492 (all elements) 0.440 (Only nonzero elements) BLAJ010101 Matrix built from structural superposition data for identifying potential Correlation with mutation matrix= 0.406 (all elements) 0.251 (Only nonzero elements) PRLA000101 Structure derived matrix (SDM) for alignment of distantly related sequences Correlation with mutation matrix= 0.475 (all elements) 0.446 (Only nonzero elements) PRLA000102 Homologous structure dereived matrix (HSDM) for alignment of distantly Correlation with mutation matrix= 0.468 (all elements) 0.435 (Only nonzero elements) DOSZ010101 Amino acid similarity matrix based on the sausage force Correlation with mutation matrix= 0.206 (all elements) 0.252 (Only nonzero elements) DOSZ010102 Normalised version of SM_SAUSAGE (Dosztanyi-Torda, 2001) Correlation with mutation matrix= 0.455 (all elements) 0.495 (Only nonzero elements) DOSZ010103 An amino acid similarity matrix based on the THREADER force field Correlation with mutation matrix= 0.447 (all elements) 0.458 (Only nonzero elements) DOSZ010104 Normalised version of SM_THREADER (Dosztanyi-Torda, 2001) Correlation with mutation matrix= 0.508 (all elements) 0.466 (Only nonzero elements) GIAG010101 Residue substitutions matrix from thermo/mesophilic to psychrophilic Correlation with mutation matrix= 0.123 (all elements) 0.322 (Only nonzero elements) DAYM780302 Log odds matrix for 40 PAMs (Dayhoff et al., 1978) Correlation with mutation matrix= 0.565 (all elements) 0.350 (Only nonzero elements) HENS920104 BLOSUM50 substitution matrix (Henikoff-Henikoff, 1992) Correlation with mutation matrix= 0.498 (all elements) 0.408 (Only nonzero elements) QUIB020101 STROMA score matrix for the alignment of known distant homologs Correlation with mutation matrix= 0.468 (all elements) 0.401 (Only nonzero elements) Correlations with unweighted double mutant paths ALTS910101 The PAM-120 matrix (Altschul, 1991) Correlation with mutation matrix= 0.080 (all elements) 0.360 (Only nonzero elements) BENS940101 Log-odds scoring matrix collected in 6.4-8.7 PAM (Benner et al., 1994) Correlation with mutation matrix= 0.073 (all elements) 0.378 (Only nonzero elements) BENS940102 Log-odds scoring matrix collected in 22-29 PAM (Benner et al., 1994) Correlation with mutation matrix= 0.051 (all elements) 0.346 (Only nonzero elements) BENS940103 Log-odds scoring matrix collected in 74-100 PAM (Benner et al., 1994) Correlation with mutation matrix= -0.007 (all elements) 0.270 (Only nonzero elements) BENS940104 Genetic code matrix (Benner et al., 1994) Correlation with mutation matrix= 0.069 (all elements) 0.421 (Only nonzero elements) CSEM940101 Residue replace ability matrix (Cserzo et al., 1994) Correlation with mutation matrix= -0.051 (all elements) 0.190 (Only nonzero elements) DAYM780301 Log odds matrix for 250 PAMs (Dayhoff et al., 1978) Correlation with mutation matrix= 0.055 (all elements) 0.307 (Only nonzero elements) FEND850101 Structure-Genetic matrix (Feng et al., 1985) Correlation with mutation matrix= 0.221 (all elements) 0.504 (Only nonzero elements) FITW660101 Mutation values for the interconversion of amino acid pairs (Fitch, 1966) Correlation with mutation matrix= -0.261 (all elements) -0.549 (Only nonzero elements) GEOD900101 Hydrophobicity scoring matrix (George et al., 1990) Correlation with mutation matrix= 0.017 (all elements) 0.110 (Only nonzero elements) GONG920101 The mutation matrix for initially aligning (Gonnet et al., 1992) Correlation with mutation matrix= -0.021 (all elements) 0.251 (Only nonzero elements) GRAR740104 Chemical distance (Grantham, 1974) Correlation with mutation matrix= -0.048 (all elements) -0.211 (Only nonzero elements) HENS920101 BLOSUM45 substitution matrix (Henikoff-Henikoff, 1992) Correlation with mutation matrix= -0.093 (all elements) 0.222 (Only nonzero elements) HENS920102 BLOSUM62 substitution matrix (Henikoff-Henikoff, 1992) Correlation with mutation matrix= -0.072 (all elements) 0.235 (Only nonzero elements) HENS920103 BLOSUM80 substitution matrix (Henikoff-Henikoff, 1992) Correlation with mutation matrix= -0.061 (all elements) 0.252 (Only nonzero elements) JOHM930101 Structure-based amino acid scoring table (Johnson-Overington, 1993) Correlation with mutation matrix= -0.034 (all elements) 0.262 (Only nonzero elements) JOND920103 The 250 PAM PET91 matrix (Jones et al., 1992) Correlation with mutation matrix= 0.057 (all elements) 0.376 (Only nonzero elements) JOND940101 The 250 PAM transmembrane protein exchange matrix (Jones et al., 1994) Correlation with mutation matrix= -0.043 (all elements) 0.216 (Only nonzero elements) KOLA920101 Conformational similarity weight matrix (Kolaskar-Kulkarni-Kale, 1992) Correlation with mutation matrix= -0.129 (all elements) -0.000 (Only nonzero elements) LEVJ860101 The secondary structure similarity matrix (Levin et al., 1986) Correlation with mutation matrix= -0.059 (all elements) 0.228 (Only nonzero elements) LUTR910101 Structure-based comparison table for outside other class (Luthy et al., 1991) Correlation with mutation matrix= -0.094 (all elements) 0.248 (Only nonzero elements) LUTR910102 Structure-based comparison table for inside other class (Luthy et al., 1991) Correlation with mutation matrix= -0.093 (all elements) 0.126 (Only nonzero elements) LUTR910103 Structure-based comparison table for outside alpha class (Luthy et al., 1991) Correlation with mutation matrix= -0.100 (all elements) 0.174 (Only nonzero elements) LUTR910104 Structure-based comparison table for inside alpha class (Luthy et al., 1991) Correlation with mutation matrix= 0.004 (all elements) 0.235 (Only nonzero elements) LUTR910105 Structure-based comparison table for outside beta class (Luthy et al., 1991) Correlation with mutation matrix= -0.039 (all elements) 0.243 (Only nonzero elements) LUTR910106 Structure-based comparison table for inside beta class (Luthy et al., 1991) Correlation with mutation matrix= -0.089 (all elements) 0.158 (Only nonzero elements) LUTR910107 Structure-based comparison table for other class (Luthy et al., 1991) Correlation with mutation matrix= -0.089 (all elements) 0.232 (Only nonzero elements) LUTR910108 Structure-based comparison table for alpha helix class (Luthy et al., 1991) Correlation with mutation matrix= -0.055 (all elements) 0.213 (Only nonzero elements) LUTR910109 Structure-based comparison table for beta strand class (Luthy et al., 1991) Correlation with mutation matrix= -0.055 (all elements) 0.236 (Only nonzero elements) MCLA710101 The similarity of pairs of amino acids (McLachlan, 1971) Correlation with mutation matrix= 0.001 (all elements) 0.297 (Only nonzero elements) MCLA720101 Chemical similarity scores (McLachlan, 1972) Correlation with mutation matrix= -0.109 (all elements) 0.249 (Only nonzero elements) MIYS930101 Base-substitution-protein-stability matrix (Miyazawa-Jernigan, 1993) Correlation with mutation matrix= 0.112 (all elements) 0.318 (Only nonzero elements) MIYT790101 Amino acid pair distance (Miyata et al., 1979) Correlation with mutation matrix= -0.060 (all elements) -0.253 (Only nonzero elements) MOHR870101 EMPAR matrix (Mohana Rao, 1987) Correlation with mutation matrix= -0.145 (all elements) 0.078 (Only nonzero elements) NIEK910101 Structure-derived correlation matrix 1 (Niefind-Schomburg, 1991) Correlation with mutation matrix= -0.143 (all elements) 0.061 (Only nonzero elements) NIEK910102 Structure-derived correlation matrix 2 (Niefind-Schomburg, 1991) Correlation with mutation matrix= -0.141 (all elements) 0.047 (Only nonzero elements) OVEJ920101 STR matrix from structure-based alignments (Overington et al., 1992) Correlation with mutation matrix= -0.032 (all elements) 0.247 (Only nonzero elements) QU_C930101 Cross-correlation coefficients of preference factors Correlation with mutation matrix= -0.209 (all elements) -0.030 (Only nonzero elements) QU_C930102 Cross-correlation coefficients of preference factors Correlation with mutation matrix= -0.075 (all elements) 0.079 (Only nonzero elements) QU_C930103 The mutant distance based on spatial preference factor (Qu et al., 1993) Correlation with mutation matrix= -0.132 (all elements) 0.091 (Only nonzero elements) RISJ880101 Scoring matrix (Risler et al., 1988) Correlation with mutation matrix= 0.186 (all elements) 0.322 (Only nonzero elements) TUDE900101 isomorphicity of replacements (Tudos et al., 1990) Correlation with mutation matrix= -0.124 (all elements) 0.196 (Only nonzero elements) AZAE970101 The single residue substitution matrix from interchanges of Correlation with mutation matrix= -0.017 (all elements) 0.159 (Only nonzero elements) AZAE970102 The substitution matrix derived from spatially conserved motifs Correlation with mutation matrix= -0.021 (all elements) 0.151 (Only nonzero elements) RIER950101 Hydrophobicity scoring matrix (Riek et al., 1995) Correlation with mutation matrix= -0.242 (all elements) -0.161 (Only nonzero elements) WEIL970101 WAC matrix constructed from amino acid comparative profiles (Wei et al., 1997) Correlation with mutation matrix= -0.194 (all elements) 0.019 (Only nonzero elements) WEIL970102 Difference matrix obtained by subtracting the BLOSUM62 from the WAC Correlation with mutation matrix= -0.048 (all elements) -0.222 (Only nonzero elements) MEHP950101 (Mehta et al., 1995) Correlation with mutation matrix= -0.013 (all elements) 0.032 (Only nonzero elements) MEHP950102 (Mehta et al., 1995) Correlation with mutation matrix= -0.009 (all elements) -0.029 (Only nonzero elements) MEHP950103 (Mehta et al., 1995) Correlation with mutation matrix= 0.043 (all elements) 0.012 (Only nonzero elements) KAPO950101 (Kapp et al., 1995) Correlation with mutation matrix= -0.059 (all elements) 0.173 (Only nonzero elements) VOGG950101 (Vogt et al., 1995) Correlation with mutation matrix= -0.021 (all elements) 0.251 (Only nonzero elements) KOSJ950101 Context-dependent optimal substitution matrices for exposed helix Correlation with mutation matrix= -0.025 (all elements) -0.024 (Only nonzero elements) KOSJ950102 Context-dependent optimal substitution matrices for exposed beta Correlation with mutation matrix= -0.021 (all elements) -0.021 (Only nonzero elements) KOSJ950103 Context-dependent optimal substitution matrices for exposed turn Correlation with mutation matrix= -0.024 (all elements) -0.016 (Only nonzero elements) KOSJ950104 Context-dependent optimal substitution matrices for exposed coil Correlation with mutation matrix= -0.012 (all elements) -0.009 (Only nonzero elements) KOSJ950105 Context-dependent optimal substitution matrices for buried helix Correlation with mutation matrix= -0.038 (all elements) -0.047 (Only nonzero elements) KOSJ950106 Context-dependent optimal substitution matrices for buried beta Correlation with mutation matrix= -0.023 (all elements) -0.032 (Only nonzero elements) KOSJ950107 Context-dependent optimal substitution matrices for buried turn Correlation with mutation matrix= -0.033 (all elements) -0.032 (Only nonzero elements) KOSJ950108 Context-dependent optimal substitution matrices for buried coil Correlation with mutation matrix= -0.037 (all elements) -0.043 (Only nonzero elements) KOSJ950109 Context-dependent optimal substitution matrices for alpha helix Correlation with mutation matrix= -0.037 (all elements) -0.039 (Only nonzero elements) KOSJ950110 Context-dependent optimal substitution matrices for beta sheet Correlation with mutation matrix= -0.022 (all elements) -0.026 (Only nonzero elements) KOSJ950111 Context-dependent optimal substitution matrices for turn Correlation with mutation matrix= -0.030 (all elements) -0.026 (Only nonzero elements) KOSJ950112 Context-dependent optimal substitution matrices for coil Correlation with mutation matrix= -0.023 (all elements) -0.025 (Only nonzero elements) KOSJ950113 Context-dependent optimal substitution matrices for exposed residues Correlation with mutation matrix= -0.027 (all elements) -0.023 (Only nonzero elements) KOSJ950114 Context-dependent optimal substitution matrices for buried residues Correlation with mutation matrix= -0.042 (all elements) -0.050 (Only nonzero elements) KOSJ950115 Context-dependent optimal substitution matrices for all residues Correlation with mutation matrix= -0.029 (all elements) -0.029 (Only nonzero elements) OVEJ920102 Environment-specific amino acid substitution matrix for alpha residues Correlation with mutation matrix= -0.097 (all elements) 0.261 (Only nonzero elements) OVEJ920103 Environment-specific amino acid substitution matrix for beta residues Correlation with mutation matrix= -0.092 (all elements) 0.241 (Only nonzero elements) OVEJ920104 Environment-specific amino acid substitution matrix for accessible Correlation with mutation matrix= -0.089 (all elements) 0.269 (Only nonzero elements) OVEJ920105 Environment-specific amino acid substitution matrix for inaccessible residues Correlation with mutation matrix= -0.134 (all elements) 0.146 (Only nonzero elements) LINK010101 Substitution matrices from an neural network model (Lin et al., 2001) Correlation with mutation matrix= -0.133 (all elements) 0.185 (Only nonzero elements) BLAJ010101 Matrix built from structural superposition data for identifying potential Correlation with mutation matrix= -0.011 (all elements) 0.117 (Only nonzero elements) PRLA000101 Structure derived matrix (SDM) for alignment of distantly related sequences Correlation with mutation matrix= -0.067 (all elements) 0.133 (Only nonzero elements) PRLA000102 Homologous structure dereived matrix (HSDM) for alignment of distantly Correlation with mutation matrix= -0.058 (all elements) 0.126 (Only nonzero elements) DOSZ010101 Amino acid similarity matrix based on the sausage force Correlation with mutation matrix= -0.025 (all elements) 0.060 (Only nonzero elements) DOSZ010102 Normalised version of SM_SAUSAGE (Dosztanyi-Torda, 2001) Correlation with mutation matrix= -0.022 (all elements) 0.061 (Only nonzero elements) DOSZ010103 An amino acid similarity matrix based on the THREADER force field Correlation with mutation matrix= -0.031 (all elements) 0.109 (Only nonzero elements) DOSZ010104 Normalised version of SM_THREADER (Dosztanyi-Torda, 2001) Correlation with mutation matrix= -0.071 (all elements) 0.111 (Only nonzero elements) GIAG010101 Residue substitutions matrix from thermo/mesophilic to psychrophilic Correlation with mutation matrix= -0.065 (all elements) -0.053 (Only nonzero elements) DAYM780302 Log odds matrix for 40 PAMs (Dayhoff et al., 1978) Correlation with mutation matrix= 0.071 (all elements) 0.339 (Only nonzero elements) HENS920104 BLOSUM50 substitution matrix (Henikoff-Henikoff, 1992) Correlation with mutation matrix= -0.103 (all elements) 0.114 (Only nonzero elements) QUIB020101 STROMA score matrix for the alignment of known distant homologs Correlation with mutation matrix= 0.068 (all elements) 0.276 (Only nonzero elements) Correlations double mutant paths weighted with human codon usage frequencies ALTS910101 The PAM-120 matrix (Altschul, 1991) Correlation with mutation matrix= -0.091 (all elements) 0.172 (Only nonzero elements) BENS940101 Log-odds scoring matrix collected in 6.4-8.7 PAM (Benner et al., 1994) Correlation with mutation matrix= -0.075 (all elements) 0.250 (Only nonzero elements) BENS940102 Log-odds scoring matrix collected in 22-29 PAM (Benner et al., 1994) Correlation with mutation matrix= -0.090 (all elements) 0.230 (Only nonzero elements) BENS940103 Log-odds scoring matrix collected in 74-100 PAM (Benner et al., 1994) Correlation with mutation matrix= -0.114 (all elements) 0.221 (Only nonzero elements) BENS940104 Genetic code matrix (Benner et al., 1994) Correlation with mutation matrix= 0.046 (all elements) 0.567 (Only nonzero elements) CSEM940101 Residue replace ability matrix (Cserzo et al., 1994) Correlation with mutation matrix= -0.168 (all elements) 0.122 (Only nonzero elements) DAYM780301 Log odds matrix for 250 PAMs (Dayhoff et al., 1978) Correlation with mutation matrix= -0.085 (all elements) 0.167 (Only nonzero elements) FEND850101 Structure-Genetic matrix (Feng et al., 1985) Correlation with mutation matrix= 0.008 (all elements) 0.266 (Only nonzero elements) FITW660101 Mutation values for the interconversion of amino acid pairs (Fitch, 1966) Correlation with mutation matrix= -0.077 (all elements) -0.324 (Only nonzero elements) GEOD900101 Hydrophobicity scoring matrix (George et al., 1990) Correlation with mutation matrix= -0.151 (all elements) -0.080 (Only nonzero elements) GONG920101 The mutation matrix for initially aligning (Gonnet et al., 1992) Correlation with mutation matrix= -0.120 (all elements) 0.216 (Only nonzero elements) GRAR740104 Chemical distance (Grantham, 1974) Correlation with mutation matrix= 0.043 (all elements) -0.158 (Only nonzero elements) HENS920101 BLOSUM45 substitution matrix (Henikoff-Henikoff, 1992) Correlation with mutation matrix= -0.224 (all elements) 0.125 (Only nonzero elements) HENS920102 BLOSUM62 substitution matrix (Henikoff-Henikoff, 1992) Correlation with mutation matrix= -0.206 (all elements) 0.139 (Only nonzero elements) HENS920103 BLOSUM80 substitution matrix (Henikoff-Henikoff, 1992) Correlation with mutation matrix= -0.205 (all elements) 0.139 (Only nonzero elements) JOHM930101 Structure-based amino acid scoring table (Johnson-Overington, 1993) Correlation with mutation matrix= -0.176 (all elements) 0.155 (Only nonzero elements) JOND920103 The 250 PAM PET91 matrix (Jones et al., 1992) Correlation with mutation matrix= -0.096 (all elements) 0.237 (Only nonzero elements) JOND940101 The 250 PAM transmembrane protein exchange matrix (Jones et al., 1994) Correlation with mutation matrix= -0.111 (all elements) 0.243 (Only nonzero elements) KOLA920101 Conformational similarity weight matrix (Kolaskar-Kulkarni-Kale, 1992) Correlation with mutation matrix= -0.151 (all elements) 0.045 (Only nonzero elements) LEVJ860101 The secondary structure similarity matrix (Levin et al., 1986) Correlation with mutation matrix= -0.240 (all elements) 0.062 (Only nonzero elements) LUTR910101 Structure-based comparison table for outside other class (Luthy et al., 1991) Correlation with mutation matrix= -0.212 (all elements) 0.174 (Only nonzero elements) LUTR910102 Structure-based comparison table for inside other class (Luthy et al., 1991) Correlation with mutation matrix= -0.155 (all elements) 0.148 (Only nonzero elements) LUTR910103 Structure-based comparison table for outside alpha class (Luthy et al., 1991) Correlation with mutation matrix= -0.200 (all elements) 0.123 (Only nonzero elements) LUTR910104 Structure-based comparison table for inside alpha class (Luthy et al., 1991) Correlation with mutation matrix= -0.165 (all elements) 0.009 (Only nonzero elements) LUTR910105 Structure-based comparison table for outside beta class (Luthy et al., 1991) Correlation with mutation matrix= -0.188 (all elements) 0.034 (Only nonzero elements) LUTR910106 Structure-based comparison table for inside beta class (Luthy et al., 1991) Correlation with mutation matrix= -0.150 (all elements) 0.199 (Only nonzero elements) LUTR910107 Structure-based comparison table for other class (Luthy et al., 1991) Correlation with mutation matrix= -0.193 (all elements) 0.190 (Only nonzero elements) LUTR910108 Structure-based comparison table for alpha helix class (Luthy et al., 1991) Correlation with mutation matrix= -0.186 (all elements) 0.082 (Only nonzero elements) LUTR910109 Structure-based comparison table for beta strand class (Luthy et al., 1991) Correlation with mutation matrix= -0.188 (all elements) 0.108 (Only nonzero elements) MCLA710101 The similarity of pairs of amino acids (McLachlan, 1971) Correlation with mutation matrix= -0.139 (all elements) 0.199 (Only nonzero elements) MCLA720101 Chemical similarity scores (McLachlan, 1972) Correlation with mutation matrix= -0.268 (all elements) 0.131 (Only nonzero elements) MIYS930101 Base-substitution-protein-stability matrix (Miyazawa-Jernigan, 1993) Correlation with mutation matrix= 0.055 (all elements) 0.338 (Only nonzero elements) MIYT790101 Amino acid pair distance (Miyata et al., 1979) Correlation with mutation matrix= 0.084 (all elements) -0.136 (Only nonzero elements) MOHR870101 EMPAR matrix (Mohana Rao, 1987) Correlation with mutation matrix= -0.239 (all elements) 0.060 (Only nonzero elements) NIEK910101 Structure-derived correlation matrix 1 (Niefind-Schomburg, 1991) Correlation with mutation matrix= -0.284 (all elements) -0.061 (Only nonzero elements) NIEK910102 Structure-derived correlation matrix 2 (Niefind-Schomburg, 1991) Correlation with mutation matrix= -0.271 (all elements) -0.059 (Only nonzero elements) OVEJ920101 STR matrix from structure-based alignments (Overington et al., 1992) Correlation with mutation matrix= -0.147 (all elements) 0.194 (Only nonzero elements) QU_C930101 Cross-correlation coefficients of preference factors Correlation with mutation matrix= -0.347 (all elements) -0.144 (Only nonzero elements) QU_C930102 Cross-correlation coefficients of preference factors Correlation with mutation matrix= -0.174 (all elements) 0.020 (Only nonzero elements) QU_C930103 The mutant distance based on spatial preference factor (Qu et al., 1993) Correlation with mutation matrix= -0.284 (all elements) -0.027 (Only nonzero elements) RISJ880101 Scoring matrix (Risler et al., 1988) Correlation with mutation matrix= -0.118 (all elements) -0.055 (Only nonzero elements) TUDE900101 isomorphicity of replacements (Tudos et al., 1990) Correlation with mutation matrix= -0.286 (all elements) 0.058 (Only nonzero elements) AZAE970101 The single residue substitution matrix from interchanges of Correlation with mutation matrix= -0.235 (all elements) -0.091 (Only nonzero elements) AZAE970102 The substitution matrix derived from spatially conserved motifs Correlation with mutation matrix= -0.222 (all elements) -0.063 (Only nonzero elements) RIER950101 Hydrophobicity scoring matrix (Riek et al., 1995) Correlation with mutation matrix= -0.117 (all elements) 0.048 (Only nonzero elements) WEIL970101 WAC matrix constructed from amino acid comparative profiles (Wei et al., 1997) Correlation with mutation matrix= -0.333 (all elements) -0.081 (Only nonzero elements) WEIL970102 Difference matrix obtained by subtracting the BLOSUM62 from the WAC Correlation with mutation matrix= 0.233 (all elements) 0.145 (Only nonzero elements) MEHP950101 (Mehta et al., 1995) Correlation with mutation matrix= -0.072 (all elements) -0.025 (Only nonzero elements) MEHP950102 (Mehta et al., 1995) Correlation with mutation matrix= 0.034 (all elements) 0.021 (Only nonzero elements) MEHP950103 (Mehta et al., 1995) Correlation with mutation matrix= 0.054 (all elements) 0.011 (Only nonzero elements) KAPO950101 (Kapp et al., 1995) Correlation with mutation matrix= -0.142 (all elements) 0.113 (Only nonzero elements) VOGG950101 (Vogt et al., 1995) Correlation with mutation matrix= -0.120 (all elements) 0.216 (Only nonzero elements) KOSJ950101 Context-dependent optimal substitution matrices for exposed helix Correlation with mutation matrix= 0.001 (all elements) 0.015 (Only nonzero elements) KOSJ950102 Context-dependent optimal substitution matrices for exposed beta Correlation with mutation matrix= 0.032 (all elements) 0.055 (Only nonzero elements) KOSJ950103 Context-dependent optimal substitution matrices for exposed turn Correlation with mutation matrix= 0.027 (all elements) 0.061 (Only nonzero elements) KOSJ950104 Context-dependent optimal substitution matrices for exposed coil Correlation with mutation matrix= 0.056 (all elements) 0.088 (Only nonzero elements) KOSJ950105 Context-dependent optimal substitution matrices for buried helix Correlation with mutation matrix= 0.015 (all elements) 0.019 (Only nonzero elements) KOSJ950106 Context-dependent optimal substitution matrices for buried beta Correlation with mutation matrix= 0.044 (all elements) 0.054 (Only nonzero elements) KOSJ950107 Context-dependent optimal substitution matrices for buried turn Correlation with mutation matrix= 0.013 (all elements) 0.033 (Only nonzero elements) KOSJ950108 Context-dependent optimal substitution matrices for buried coil Correlation with mutation matrix= 0.014 (all elements) 0.025 (Only nonzero elements) KOSJ950109 Context-dependent optimal substitution matrices for alpha helix Correlation with mutation matrix= 0.019 (all elements) 0.038 (Only nonzero elements) KOSJ950110 Context-dependent optimal substitution matrices for beta sheet Correlation with mutation matrix= 0.038 (all elements) 0.054 (Only nonzero elements) KOSJ950111 Context-dependent optimal substitution matrices for turn Correlation with mutation matrix= 0.016 (all elements) 0.042 (Only nonzero elements) KOSJ950112 Context-dependent optimal substitution matrices for coil Correlation with mutation matrix= 0.041 (all elements) 0.063 (Only nonzero elements) KOSJ950113 Context-dependent optimal substitution matrices for exposed residues Correlation with mutation matrix= 0.033 (all elements) 0.063 (Only nonzero elements) KOSJ950114 Context-dependent optimal substitution matrices for buried residues Correlation with mutation matrix= 0.018 (all elements) 0.030 (Only nonzero elements) KOSJ950115 Context-dependent optimal substitution matrices for all residues Correlation with mutation matrix= 0.025 (all elements) 0.048 (Only nonzero elements) OVEJ920102 Environment-specific amino acid substitution matrix for alpha residues Correlation with mutation matrix= -0.315 (all elements) 0.055 (Only nonzero elements) OVEJ920103 Environment-specific amino acid substitution matrix for beta residues Correlation with mutation matrix= -0.299 (all elements) 0.053 (Only nonzero elements) OVEJ920104 Environment-specific amino acid substitution matrix for accessible Correlation with mutation matrix= -0.297 (all elements) 0.095 (Only nonzero elements) OVEJ920105 Environment-specific amino acid substitution matrix for inaccessible residues Correlation with mutation matrix= -0.355 (all elements) -0.033 (Only nonzero elements) LINK010101 Substitution matrices from an neural network model (Lin et al., 2001) Correlation with mutation matrix= -0.362 (all elements) 0.003 (Only nonzero elements) BLAJ010101 Matrix built from structural superposition data for identifying potential Correlation with mutation matrix= -0.144 (all elements) 0.078 (Only nonzero elements) PRLA000101 Structure derived matrix (SDM) for alignment of distantly related sequences Correlation with mutation matrix= -0.168 (all elements) 0.177 (Only nonzero elements) PRLA000102 Homologous structure dereived matrix (HSDM) for alignment of distantly Correlation with mutation matrix= -0.151 (all elements) 0.197 (Only nonzero elements) DOSZ010101 Amino acid similarity matrix based on the sausage force Correlation with mutation matrix= -0.093 (all elements) 0.064 (Only nonzero elements) DOSZ010102 Normalised version of SM_SAUSAGE (Dosztanyi-Torda, 2001) Correlation with mutation matrix= -0.075 (all elements) 0.129 (Only nonzero elements) DOSZ010103 An amino acid similarity matrix based on the THREADER force field Correlation with mutation matrix= -0.163 (all elements) 0.148 (Only nonzero elements) DOSZ010104 Normalised version of SM_THREADER (Dosztanyi-Torda, 2001) Correlation with mutation matrix= -0.190 (all elements) 0.176 (Only nonzero elements) GIAG010101 Residue substitutions matrix from thermo/mesophilic to psychrophilic Correlation with mutation matrix= 0.083 (all elements) 0.137 (Only nonzero elements) DAYM780302 Log odds matrix for 40 PAMs (Dayhoff et al., 1978) Correlation with mutation matrix= -0.104 (all elements) 0.247 (Only nonzero elements) HENS920104 BLOSUM50 substitution matrix (Henikoff-Henikoff, 1992) Correlation with mutation matrix= -0.214 (all elements) 0.187 (Only nonzero elements) QUIB020101 STROMA score matrix for the alignment of known distant homologs Correlation with mutation matrix= -0.055 (all elements) 0.252 (Only nonzero elements)