125 lines
10 KiB
Text
125 lines
10 KiB
Text
ALTS910101 The PAM-120 matrix (Altschul, 1991)
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AZAE970101 The single residue substitution matrix from interchanges of spatially neighbouring residues (Azarya-Sprinzak et al., 1997)
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AZAE970102 The substitution matrix derived from spatially conserved motifs (Azarya-Sprinzak et al., 1997)
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BASU010101 Optimization-based potential derived by the modified perceptron criterion
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BENS940101 Log-odds scoring matrix collected in 6.4-8.7 PAM (Benner et al., 1994)
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BENS940102 Log-odds scoring matrix collected in 22-29 PAM (Benner et al., 1994)
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BENS940103 Log-odds scoring matrix collected in 74-100 PAM (Benner et al., 1994)
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BENS940104 Genetic code matrix (Benner et al., 1994)
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BETM990101 Modified version of the Miyazawa-Jernigan transfer energy
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BLAJ010101 Matrix built from structural superposition data for identifying potential remote homologues (Blake-Cohen, 2001)
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BONM030101 Quasichemical statistical potential for the antiparallel orientation of interacting side groups
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BONM030102 Quasichemical statistical potential for the intermediate orientation of interacting side groups
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BONM030103 Quasichemical statistical potential for the parallel orientation of interacting side groups
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BONM030104 Distances between centers of interacting side chains in the antiparallel orientation
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BONM030105 Distances between centers of interacting side chains in the intermediate orientation
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BONM030106 Distances between centers of interacting side chains in the parallel orientation
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BRYS930101 Distance-dependent statistical potential (only energies of contacts within 0-5 Angstrooms are included)
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CROG050101 Substitution matrix computed from the Dirichlet Mixture Model (Crooks-Brenner, 2005)
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CSEM940101 Residue replace ability matrix (Cserzo et al., 1994)
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DAYM780301 Log odds matrix for 250 PAMs (Dayhoff et al., 1978)
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DAYM780302 Log odds matrix for 40 PAMs (Dayhoff et al., 1978)
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DOSZ010101 Amino acid similarity matrix based on the sausage force field (Dosztanyi-Torda, 2001)
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DOSZ010102 Normalised version of SM_SAUSAGE (Dosztanyi-Torda, 2001)
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DOSZ010103 An amino acid similarity matrix based on the THREADER force field (Dosztanyi-Torda, 2001)
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DOSZ010104 Normalised version of SM_THREADER (Dosztanyi-Torda, 2001)
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FEND850101 Structure-Genetic matrix (Feng et al., 1985)
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FITW660101 Mutation values for the interconversion of amino acid pairs (Fitch, 1966)
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GEOD900101 Hydrophobicity scoring matrix (George et al., 1990)
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GIAG010101 Residue substitutions matrix from thermo/mesophilic to psychrophilic enzymes (Gianese et al., 2001)
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GODA950101 Quasichemical statistical potential derived from buried contacts
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GONG920101 The mutation matrix for initially aligning (Gonnet et al., 1992)
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GRAR740104 Chemical distance (Grantham, 1974)
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HENS920101 BLOSUM45 substitution matrix (Henikoff-Henikoff, 1992)
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HENS920102 BLOSUM62 substitution matrix (Henikoff-Henikoff, 1992)
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HENS920103 BLOSUM80 substitution matrix (Henikoff-Henikoff, 1992)
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HENS920104 BLOSUM50 substitution matrix (Henikoff-Henikoff, 1992)
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JOHM930101 Structure-based amino acid scoring table (Johnson-Overington, 1993)
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JOND920103 The 250 PAM PET91 matrix (Jones et al., 1992)
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JOND940101 The 250 PAM transmembrane protein exchange matrix (Jones et al., 1994)
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KANM000101 Substitution matrix (OPTIMA) derived by maximizing discrimination between homologs and non-homologs (Kann et al., 2000)
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KAPO950101 (Kapp et al., 1995)
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KESO980101 Quasichemical transfer energy derived from interfacial regions of protein-protein complexes
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KESO980102 Quasichemical energy in an average protein environment derived from interfacial regions of protein-protein complexes
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KOLA920101 Conformational similarity weight matrix (Kolaskar-Kulkarni-Kale, 1992)
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KOLA930101 Statistical potential derived by the quasichemical approximation
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KOSJ950115 Context-dependent optimal substitution matrices for all residues (Koshi-Goldstein, 1995)
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LEVJ860101 The secondary structure similarity matrix (Levin et al., 1986)
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LINK010101 Substitution matrices from an neural network model (Lin et al., 2001)
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LIWA970101 Modified version of the Miyazawa-Jernigan transfer energy
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LUTR910101 Structure-based comparison table for outside other class (Luthy et al., 1991)
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LUTR910102 Structure-based comparison table for inside other class (Luthy et al., 1991)
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LUTR910103 Structure-based comparison table for outside alpha class (Luthy et al., 1991)
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LUTR910104 Structure-based comparison table for inside alpha class (Luthy et al., 1991)
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LUTR910105 Structure-based comparison table for outside beta class (Luthy et al., 1991)
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LUTR910106 Structure-based comparison table for inside beta class (Luthy et al., 1991)
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LUTR910107 Structure-based comparison table for other class (Luthy et al., 1991)
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LUTR910108 Structure-based comparison table for alpha helix class (Luthy et al., 1991)
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LUTR910109 Structure-based comparison table for beta strand class (Luthy et al., 1991)
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MCLA710101 The similarity of pairs of amino acids (McLachlan, 1971)
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MCLA720101 Chemical similarity scores (McLachlan, 1972)
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MEHP950101 (Mehta et al., 1995)
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MEHP950102 (Mehta et al., 1995)
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MEHP950103 (Mehta et al., 1995)
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MICC010101 Optimization-derived potential
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MIRL960101 Statistical potential derived by the maximization of the harmonic mean of Z scores
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MIYS850102 Quasichemical energy of transfer of amino acids from water to the protein environment
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MIYS850103 Quasichemical energy of interactions in an average buried environment
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MIYS930101 Base-substitution-protein-stability matrix (Miyazawa-Jernigan, 1993)
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MIYS960101 Quasichemical energy of transfer of amino acids from water to the protein environment
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MIYS960102 Quasichemical energy of interactions in an average buried environment
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MIYS960103 Number of contacts between side chains derived from 1168 x-ray protein structures
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MIYS990106 Quasichemical energy of transfer of amino acids from water to the protein environment
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MIYS990107 Quasichemical energy of interactions in an average buried environment
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MIYT790101 Amino acid pair distance (Miyata et al., 1979)
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MOHR870101 EMPAR matrix (Mohana Rao, 1987)
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MOOG990101 Quasichemical potential derived from interfacial regions of protein-protein complexes
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MUET010101 Non-symmetric substitution matrix (SLIM) for detection of homologous transmembrane proteins (Mueller et al., 2001)
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MUET020101 Substitution matrix (VTML160) obtained by maximum likelihood estimation (Mueller et al., 2002)
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MUET020102 Substitution matrix (VTML250) obtained by maximum likelihood estimation (Mueller et al., 2002)
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NAOD960101 Substitution matrix derived from the single residue interchanges at spatially conserved regions of proteins (Naor et al., 1996)
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NGPC000101 Substitution matrix (PHAT) built from hydrophobic and transmembrane regions of the Blocks database (Ng et al., 2000)
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NIEK910101 Structure-derived correlation matrix 1 (Niefind-Schomburg, 1991)
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NIEK910102 Structure-derived correlation matrix 2 (Niefind-Schomburg, 1991)
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OGAK980101 Substitution matrix derived from structural alignments by maximizing entropy (Ogata et al., 1998)
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OVEJ920101 STR matrix from structure-based alignments (Overington et al., 1992)
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OVEJ920102 Environment-specific amino acid substitution matrix for alpha residues (Overington et al., 1992)
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OVEJ920103 Environment-specific amino acid substitution matrix for beta residues (Overington et al., 1992)
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PARB960101 Statistical contact potential derived by the quasichemical approximation
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PARB960102 Modified version of the Miyazawa-Jernigan transfer energy
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PRLA000101 Structure derived matrix (SDM) for alignment of distantly related sequences (Prlic et al., 2000)
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PRLA000102 Homologous structure dereived matrix (HSDM) for alignment of distantly related sequences (Prlic et al., 2000)
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QUIB020101 STROMA score matrix for the alignment of known distant homologs (Qian-Goldstein, 2002)
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QU_C930101 Cross-correlation coefficients of preference factors main chain (Qu et al., 1993)
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QU_C930102 Cross-correlation coefficients of preference factors side chain (Qu et al., 1993)
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QU_C930103 The mutant distance based on spatial preference factor (Qu et al., 1993)
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RIER950101 Hydrophobicity scoring matrix (Riek et al., 1995)
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RISJ880101 Scoring matrix (Risler et al., 1988)
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ROBB790102 Interaction energies derived from side chain contacts in the interiors of known protein structures
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RUSR970101 Substitution matrix based on structural alignments of analogous proteins (Russell et al., 1997)
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RUSR970102 Substitution matrix based on structural alignments of remote homolous proteins (Russell et al., 1997)
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RUSR970103 Substitution matrix based on structural alignments of analogous and remote homolous proteins (Russell et al., 1997)
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SIMK990101 Distance-dependent statistical potential (contacts within 0-5 Angstrooms)
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SIMK990102 Distance-dependent statistical potential (contacts within 5-7.5 Angstrooms)
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SIMK990103 Distance-dependent statistical potential (contacts within 7.5-10 Angstrooms)
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SIMK990104 Distance-dependent statistical potential (contacts within 10-12 Angstrooms)
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SIMK990105 Distance-dependent statistical potential (contacts longer than 12 Angstrooms)
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SKOJ000101 Statistical quasichemical potential with the partially composition-corrected pair scale
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SKOJ000102 Statistical quasichemical potential with the composition-corrected pair scale
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SKOJ970101 Statistical potential derived by the quasichemical approximation
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TANS760101 Statistical contact potential derived from 25 x-ray protein structures
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TANS760102 Number of contacts between side chains derived from 25 x-ray protein structures
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THOP960101 Mixed quasichemical and optimization-based protein contact potential
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TOBD000101 Optimization-derived potential obtained for small set of decoys
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TOBD000102 Optimization-derived potential obtained for large set of decoys
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TUDE900101 isomorphicity of replacements (Tudos et al., 1990)
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VENM980101 Statistical potential derived by the maximization of the perceptron criterion
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VOGG950101 (Vogt et al., 1995)
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WEIL970101 WAC matrix constructed from amino acid comparative profiles (Wei et al., 1997)
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WEIL970102 Difference matrix obtained by subtracting the BLOSUM62 from the WAC matrix (Wei et al., 1997)
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ZHAC000101 Environment-dependent residue contact energies (rows = helix, cols = helix)
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ZHAC000102 Environment-dependent residue contact energies (rows = helix, cols = strand)
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ZHAC000103 Environment-dependent residue contact energies (rows = helix, cols = coil)
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ZHAC000104 Environment-dependent residue contact energies (rows = strand, cols = strand)
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ZHAC000105 Environment-dependent residue contact energies (rows = strand, cols = coil)
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ZHAC000106 Environment-dependent residue contact energies (rows = coil, cols = coil)
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