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)
BASU010101 Optimization-based potential derived by the modified perceptron criterion
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)
BETM990101 Modified version of the Miyazawa-Jernigan transfer energy
BLAJ010101 Matrix built from structural superposition data for identifying potential remote homologues (Blake-Cohen, 2001)
BONM030101 Quasichemical statistical potential for the antiparallel orientation of interacting side groups
BONM030102 Quasichemical statistical potential for the intermediate orientation of interacting side groups
BONM030103 Quasichemical statistical potential for the parallel orientation of interacting side groups
BONM030104 Distances between centers of interacting side chains in the antiparallel orientation
BONM030105 Distances between centers of interacting side chains in the intermediate orientation
BONM030106 Distances between centers of interacting side chains in the parallel orientation
BRYS930101 Distance-dependent statistical potential (only energies of contacts within 0-5 Angstrooms are included)
CROG050101 Substitution matrix computed from the Dirichlet Mixture Model (Crooks-Brenner, 2005)
CSEM940101 Residue replace ability matrix (Cserzo et al., 1994)
DAYM780301 Log odds matrix for 250 PAMs (Dayhoff et al., 1978)
DAYM780302 Log odds matrix for 40 PAMs (Dayhoff et al., 1978)
DOSZ010101 Amino acid similarity matrix based on the sausage force field (Dosztanyi-Torda, 2001)
DOSZ010102 Normalised version of SM_SAUSAGE (Dosztanyi-Torda, 2001)
DOSZ010103 An amino acid similarity matrix based on the THREADER force field (Dosztanyi-Torda, 2001)
DOSZ010104 Normalised version of SM_THREADER (Dosztanyi-Torda, 2001)
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)
GIAG010101 Residue substitutions matrix from thermo/mesophilic to psychrophilic enzymes (Gianese et al., 2001)
GODA950101 Quasichemical statistical potential derived from  buried contacts
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)
HENS920104 BLOSUM50 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)
KANM000101 Substitution matrix (OPTIMA) derived by maximizing discrimination between homologs and non-homologs (Kann et al., 2000)
KAPO950101 (Kapp et al., 1995)
KESO980101 Quasichemical transfer energy derived from interfacial regions of protein-protein complexes
KESO980102 Quasichemical energy in an average protein environment derived from interfacial regions of protein-protein complexes
KOLA920101 Conformational similarity weight matrix (Kolaskar-Kulkarni-Kale, 1992)
KOLA930101 Statistical potential derived by the quasichemical approximation
KOSJ950115 Context-dependent optimal substitution matrices for all residues (Koshi-Goldstein, 1995)
LEVJ860101 The secondary structure similarity matrix (Levin et al., 1986)
LINK010101 Substitution matrices from an neural network model (Lin et al., 2001)
LIWA970101 Modified version of the Miyazawa-Jernigan transfer energy
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)
MICC010101 Optimization-derived potential
MIRL960101 Statistical potential derived by the maximization of the harmonic mean of Z scores
MIYS850102 Quasichemical energy of transfer of amino acids from water to the protein environment
MIYS850103 Quasichemical energy of interactions in an average buried environment
MIYS930101 Base-substitution-protein-stability matrix (Miyazawa-Jernigan, 1993)
MIYS960101 Quasichemical energy of transfer of amino acids from water to the protein environment
MIYS960102 Quasichemical energy of interactions in an average buried environment
MIYS960103 Number of contacts between side chains derived from 1168 x-ray protein structures
MIYS990106 Quasichemical energy of transfer of amino acids from water to the protein environment
MIYS990107 Quasichemical energy of interactions in an average buried environment
MIYT790101 Amino acid pair distance (Miyata et al., 1979)
MOHR870101 EMPAR matrix (Mohana Rao, 1987)
MOOG990101 Quasichemical potential derived from interfacial regions of protein-protein complexes
MUET010101 Non-symmetric substitution matrix (SLIM) for detection of homologous transmembrane proteins (Mueller et al., 2001)
MUET020101 Substitution matrix (VTML160) obtained by maximum likelihood estimation (Mueller et al., 2002)
MUET020102 Substitution matrix (VTML250) obtained by maximum likelihood estimation (Mueller et al., 2002)
NAOD960101 Substitution matrix derived from the single residue interchanges at spatially conserved regions of proteins (Naor et al., 1996)
NGPC000101 Substitution matrix (PHAT) built from hydrophobic and transmembrane regions of the Blocks database (Ng et al., 2000)
NIEK910101 Structure-derived correlation matrix 1 (Niefind-Schomburg, 1991)
NIEK910102 Structure-derived correlation matrix 2 (Niefind-Schomburg, 1991)
OGAK980101 Substitution matrix derived from structural alignments by maximizing entropy (Ogata et al., 1998)
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)
PARB960101 Statistical contact potential derived by the quasichemical approximation
PARB960102 Modified version of the Miyazawa-Jernigan transfer energy
PRLA000101 Structure derived matrix (SDM) for alignment of distantly related sequences (Prlic et al., 2000)
PRLA000102 Homologous structure dereived matrix (HSDM) for alignment of distantly related sequences (Prlic et al., 2000)
QUIB020101 STROMA score matrix for the alignment of known distant homologs (Qian-Goldstein, 2002)
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)
ROBB790102 Interaction energies derived from side chain contacts in the interiors of known protein structures
RUSR970101 Substitution matrix based on structural alignments of analogous proteins (Russell et al., 1997)
RUSR970102 Substitution matrix based on structural alignments of remote homolous proteins (Russell et al., 1997)
RUSR970103 Substitution matrix based on structural alignments of analogous and remote homolous proteins (Russell et al., 1997)
SIMK990101 Distance-dependent statistical potential (contacts within 0-5 Angstrooms)
SIMK990102 Distance-dependent statistical potential (contacts within 5-7.5 Angstrooms)
SIMK990103 Distance-dependent statistical potential (contacts within 7.5-10 Angstrooms)
SIMK990104 Distance-dependent statistical potential (contacts within 10-12 Angstrooms)
SIMK990105 Distance-dependent statistical potential (contacts longer than 12 Angstrooms)
SKOJ000101 Statistical quasichemical potential with the partially composition-corrected pair scale
SKOJ000102 Statistical quasichemical potential with the composition-corrected pair scale
SKOJ970101 Statistical potential derived by the quasichemical approximation
TANS760101 Statistical contact potential derived from 25 x-ray protein structures
TANS760102 Number of contacts between side chains derived from 25 x-ray protein structures
THOP960101 Mixed quasichemical and optimization-based protein contact potential
TOBD000101 Optimization-derived potential obtained for small set of decoys
TOBD000102 Optimization-derived potential obtained for large set of decoys
TUDE900101 isomorphicity of replacements (Tudos et al., 1990)
VENM980101 Statistical potential derived by the maximization of the perceptron criterion
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)
ZHAC000101 Environment-dependent residue contact energies (rows = helix, cols = helix)
ZHAC000102 Environment-dependent residue contact energies (rows = helix, cols = strand)
ZHAC000103 Environment-dependent residue contact energies (rows = helix, cols = coil)
ZHAC000104 Environment-dependent residue contact energies (rows = strand, cols = strand)
ZHAC000105 Environment-dependent residue contact energies (rows = strand, cols = coil)
ZHAC000106 Environment-dependent residue contact energies (rows = coil, cols = coil)
