added scripts and files to make AA index work for all drug targets, add header to the aa index output and fetch the aa index headers
This commit is contained in:
parent
03321c261e
commit
1204f1faba
14 changed files with 1746 additions and 1969 deletions
File diff suppressed because it is too large
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1
scripts/aa_index_scripts/ADD_aa_header.csv
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scripts/aa_index_scripts/ADD_aa_header.csv
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mutationinformation,ALTS910101,AZAE970101,AZAE970102,BASU010101,BENS940101,BENS940102,BENS940103,BENS940104,BETM990101,BLAJ010101,BONM030101,BONM030102,BONM030103,BONM030104,BONM030105,BONM030106,BRYS930101,CROG050101,CSEM940101,DAYM780301,DAYM780302,DOSZ010101,DOSZ010102,DOSZ010103,DOSZ010104,FEND850101,FITW660101,GEOD900101,GIAG010101,GODA950101,GONG920101,GRAR740104,HENS920101,HENS920102,HENS920103,HENS920104,JOHM930101,JOND920103,JOND940101,KANM000101,KAPO950101,KESO980101,KESO980102,KOLA920101,KOLA930101,KOSJ950100_RSA_SST,KOSJ950100_SST,KOSJ950110_RSA,KOSJ950115,LEVJ860101,LINK010101,LIWA970101,LUTR910101,LUTR910102,LUTR910103,LUTR910104,LUTR910105,LUTR910106,LUTR910107,LUTR910108,LUTR910109,MCLA710101,MCLA720101,MEHP950101,MEHP950102,MEHP950103,MICC010101,MIRL960101,MIYS850102,MIYS850103,MIYS930101,MIYS960101,MIYS960102,MIYS960103,MIYS990106,MIYS990107,MIYT790101,MOHR870101,MOOG990101,MUET010101,MUET020101,MUET020102,NAOD960101,NGPC000101,NIEK910101,NIEK910102,OGAK980101,OVEJ920100_RSA,OVEJ920101,OVEJ920102,OVEJ920103,PARB960101,PARB960102,PRLA000101,PRLA000102,QUIB020101,QU_C930101,QU_C930102,QU_C930103,RIER950101,RISJ880101,ROBB790102,RUSR970101,RUSR970102,RUSR970103,SIMK990101,SIMK990102,SIMK990103,SIMK990104,SIMK990105,SKOJ000101,SKOJ000102,SKOJ970101,TANS760101,TANS760102,THOP960101,TOBD000101,TOBD000102,TUDE900101,VENM980101,VOGG950101,WEIL970101,WEIL970102,ZHAC000101,ZHAC000102,ZHAC000103,ZHAC000104,ZHAC000105,ZHAC000106
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scripts/aa_index_scripts/aa_header.csv
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scripts/aa_index_scripts/aa_header.csv
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ALTS910101,AZAE970101,AZAE970102,BASU010101,BENS940101,BENS940102,BENS940103,BENS940104,BETM990101,BLAJ010101,BONM030101,BONM030102,BONM030103,BONM030104,BONM030105,BONM030106,BRYS930101,CROG050101,CSEM940101,DAYM780301,DAYM780302,DOSZ010101,DOSZ010102,DOSZ010103,DOSZ010104,FEND850101,FITW660101,GEOD900101,GIAG010101,GODA950101,GONG920101,GRAR740104,HENS920101,HENS920102,HENS920103,HENS920104,JOHM930101,JOND920103,JOND940101,KANM000101,KAPO950101,KESO980101,KESO980102,KOLA920101,KOLA930101,KOSJ950100_RSA_SST,KOSJ950100_SST,KOSJ950110_RSA,KOSJ950115,LEVJ860101,LINK010101,LIWA970101,LUTR910101,LUTR910102,LUTR910103,LUTR910104,LUTR910105,LUTR910106,LUTR910107,LUTR910108,LUTR910109,MCLA710101,MCLA720101,MEHP950101,MEHP950102,MEHP950103,MICC010101,MIRL960101,MIYS850102,MIYS850103,MIYS930101,MIYS960101,MIYS960102,MIYS960103,MIYS990106,MIYS990107,MIYT790101,MOHR870101,MOOG990101,MUET010101,MUET020101,MUET020102,NAOD960101,NGPC000101,NIEK910101,NIEK910102,OGAK980101,OVEJ920100_RSA,OVEJ920101,OVEJ920102,OVEJ920103,PARB960101,PARB960102,PRLA000101,PRLA000102,QUIB020101,QU_C930101,QU_C930102,QU_C930103,RIER950101,RISJ880101,ROBB790102,RUSR970101,RUSR970102,RUSR970103,SIMK990101,SIMK990102,SIMK990103,SIMK990104,SIMK990105,SKOJ000101,SKOJ000102,SKOJ970101,TANS760101,TANS760102,THOP960101,TOBD000101,TOBD000102,TUDE900101,VENM980101,VOGG950101,WEIL970101,WEIL970102,ZHAC000101,ZHAC000102,ZHAC000103,ZHAC000104,ZHAC000105,ZHAC000106
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scripts/aa_index_scripts/aa_headerMapping.sh
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scripts/aa_index_scripts/aa_headerMapping.sh
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#!/bin/sh
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# get the list of AA indices and then combine these into one file
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wget -c https://www.genome.jp/aaindex/AAindex/list_of_indices https://www.genome.jp/aaindex/AAindex/list_of_potentials https://www.genome.jp/aaindex/AAindex/list_of_matrices
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cat list_of_* > combined_aa_list
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# get the description for the header used in our script
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for i in $(cat aa_headerT.csv); do
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grep $i combined_aa_list >> aa_headerNames
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done
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scripts/aa_index_scripts/aa_headerNames.txt
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scripts/aa_index_scripts/aa_headerNames.txt
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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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scripts/aa_index_scripts/aa_headerT.csv
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ALTS910101
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AZAE970101
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AZAE970102
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BASU010101
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BENS940101
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BENS940102
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BENS940103
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BENS940104
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BETM990101
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BLAJ010101
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BONM030101
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BONM030102
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BONM030103
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BONM030104
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BONM030105
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BONM030106
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BRYS930101
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CROG050101
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CSEM940101
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DAYM780301
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DAYM780302
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DOSZ010101
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DOSZ010102
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DOSZ010103
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DOSZ010104
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FEND850101
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FITW660101
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GEOD900101
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GIAG010101
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GODA950101
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GONG920101
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GRAR740104
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HENS920101
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HENS920102
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HENS920103
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HENS920104
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JOHM930101
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JOND920103
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JOND940101
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KANM000101
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KAPO950101
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KESO980101
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KESO980102
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KOLA920101
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KOLA930101
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KOSJ950100_RSA_SST
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KOSJ950100_SST
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KOSJ950110_RSA
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KOSJ950115
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LEVJ860101
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LINK010101
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LIWA970101
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LUTR910101
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LUTR910102
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LUTR910103
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LUTR910104
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LUTR910105
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LUTR910106
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LUTR910107
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LUTR910108
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LUTR910109
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MCLA710101
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MCLA720101
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MEHP950101
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MEHP950102
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MEHP950103
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MICC010101
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MIRL960101
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MIYS850102
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MIYS850103
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MIYS930101
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MIYS960101
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MIYS960102
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MIYS960103
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MIYS990106
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MIYS990107
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MIYT790101
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MOHR870101
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MOOG990101
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MUET010101
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MUET020101
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MUET020102
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NAOD960101
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NGPC000101
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NIEK910101
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NIEK910102
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OGAK980101
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OVEJ920100_RSA
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OVEJ920101
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OVEJ920102
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OVEJ920103
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PARB960101
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PARB960102
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PRLA000101
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PRLA000102
|
||||||
|
QUIB020101
|
||||||
|
QU_C930101
|
||||||
|
QU_C930102
|
||||||
|
QU_C930103
|
||||||
|
RIER950101
|
||||||
|
RISJ880101
|
||||||
|
ROBB790102
|
||||||
|
RUSR970101
|
||||||
|
RUSR970102
|
||||||
|
RUSR970103
|
||||||
|
SIMK990101
|
||||||
|
SIMK990102
|
||||||
|
SIMK990103
|
||||||
|
SIMK990104
|
||||||
|
SIMK990105
|
||||||
|
SKOJ000101
|
||||||
|
SKOJ000102
|
||||||
|
SKOJ970101
|
||||||
|
TANS760101
|
||||||
|
TANS760102
|
||||||
|
THOP960101
|
||||||
|
TOBD000101
|
||||||
|
TOBD000102
|
||||||
|
TUDE900101
|
||||||
|
VENM980101
|
||||||
|
VOGG950101
|
||||||
|
WEIL970101
|
||||||
|
WEIL970102
|
||||||
|
ZHAC000101
|
||||||
|
ZHAC000102
|
||||||
|
ZHAC000103
|
||||||
|
ZHAC000104
|
||||||
|
ZHAC000105
|
||||||
|
ZHAC000106
|
||||||
|
722
scripts/aa_index_scripts/combined_aa_list
Normal file
722
scripts/aa_index_scripts/combined_aa_list
Normal file
|
|
@ -0,0 +1,722 @@
|
||||||
|
List of 566 Amino Acid Indices in AAindex ver.9.2
|
||||||
|
|
||||||
|
The columns correspond to the AAindex accession number and the description of
|
||||||
|
each index.
|
||||||
|
|
||||||
|
ANDN920101 alpha-CH chemical shifts (Andersen et al., 1992)
|
||||||
|
ARGP820101 Hydrophobicity index (Argos et al., 1982)
|
||||||
|
ARGP820102 Signal sequence helical potential (Argos et al., 1982)
|
||||||
|
ARGP820103 Membrane-buried preference parameters (Argos et al., 1982)
|
||||||
|
BEGF750101 Conformational parameter of inner helix (Beghin-Dirkx, 1975)
|
||||||
|
BEGF750102 Conformational parameter of beta-structure (Beghin-Dirkx, 1975)
|
||||||
|
BEGF750103 Conformational parameter of beta-turn (Beghin-Dirkx, 1975)
|
||||||
|
BHAR880101 Average flexibility indices (Bhaskaran-Ponnuswamy, 1988)
|
||||||
|
BIGC670101 Residue volume (Bigelow, 1967)
|
||||||
|
BIOV880101 Information value for accessibility; average fraction 35% (Biou et al., 1988)
|
||||||
|
BIOV880102 Information value for accessibility; average fraction 23% (Biou et al., 1988)
|
||||||
|
BROC820101 Retention coefficient in TFA (Browne et al., 1982)
|
||||||
|
BROC820102 Retention coefficient in HFBA (Browne et al., 1982)
|
||||||
|
BULH740101 Transfer free energy to surface (Bull-Breese, 1974)
|
||||||
|
BULH740102 Apparent partial specific volume (Bull-Breese, 1974)
|
||||||
|
BUNA790101 alpha-NH chemical shifts (Bundi-Wuthrich, 1979)
|
||||||
|
BUNA790102 alpha-CH chemical shifts (Bundi-Wuthrich, 1979)
|
||||||
|
BUNA790103 Spin-spin coupling constants 3JHalpha-NH (Bundi-Wuthrich, 1979)
|
||||||
|
BURA740101 Normalized frequency of alpha-helix (Burgess et al., 1974)
|
||||||
|
BURA740102 Normalized frequency of extended structure (Burgess et al., 1974)
|
||||||
|
CHAM810101 Steric parameter (Charton, 1981)
|
||||||
|
CHAM820101 Polarizability parameter (Charton-Charton, 1982)
|
||||||
|
CHAM820102 Free energy of solution in water, kcal/mole (Charton-Charton, 1982)
|
||||||
|
CHAM830101 The Chou-Fasman parameter of the coil conformation (Charton-Charton, 1983)
|
||||||
|
CHAM830102 A parameter defined from the residuals obtained from the best correlation of the Chou-Fasman parameter of beta-sheet (Charton-Charton, 1983)
|
||||||
|
CHAM830103 The number of atoms in the side chain labelled 1+1 (Charton-Charton, 1983)
|
||||||
|
CHAM830104 The number of atoms in the side chain labelled 2+1 (Charton-Charton, 1983)
|
||||||
|
CHAM830105 The number of atoms in the side chain labelled 3+1 (Charton-Charton, 1983)
|
||||||
|
CHAM830106 The number of bonds in the longest chain (Charton-Charton, 1983)
|
||||||
|
CHAM830107 A parameter of charge transfer capability (Charton-Charton, 1983)
|
||||||
|
CHAM830108 A parameter of charge transfer donor capability (Charton-Charton, 1983)
|
||||||
|
CHOC750101 Average volume of buried residue (Chothia, 1975)
|
||||||
|
CHOC760101 Residue accessible surface area in tripeptide (Chothia, 1976)
|
||||||
|
CHOC760102 Residue accessible surface area in folded protein (Chothia, 1976)
|
||||||
|
CHOC760103 Proportion of residues 95% buried (Chothia, 1976)
|
||||||
|
CHOC760104 Proportion of residues 100% buried (Chothia, 1976)
|
||||||
|
CHOP780101 Normalized frequency of beta-turn (Chou-Fasman, 1978a)
|
||||||
|
CHOP780201 Normalized frequency of alpha-helix (Chou-Fasman, 1978b)
|
||||||
|
CHOP780202 Normalized frequency of beta-sheet (Chou-Fasman, 1978b)
|
||||||
|
CHOP780203 Normalized frequency of beta-turn (Chou-Fasman, 1978b)
|
||||||
|
CHOP780204 Normalized frequency of N-terminal helix (Chou-Fasman, 1978b)
|
||||||
|
CHOP780205 Normalized frequency of C-terminal helix (Chou-Fasman, 1978b)
|
||||||
|
CHOP780206 Normalized frequency of N-terminal non helical region (Chou-Fasman, 1978b)
|
||||||
|
CHOP780207 Normalized frequency of C-terminal non helical region (Chou-Fasman, 1978b)
|
||||||
|
CHOP780208 Normalized frequency of N-terminal beta-sheet (Chou-Fasman, 1978b)
|
||||||
|
CHOP780209 Normalized frequency of C-terminal beta-sheet (Chou-Fasman, 1978b)
|
||||||
|
CHOP780210 Normalized frequency of N-terminal non beta region (Chou-Fasman, 1978b)
|
||||||
|
CHOP780211 Normalized frequency of C-terminal non beta region (Chou-Fasman, 1978b)
|
||||||
|
CHOP780212 Frequency of the 1st residue in turn (Chou-Fasman, 1978b)
|
||||||
|
CHOP780213 Frequency of the 2nd residue in turn (Chou-Fasman, 1978b)
|
||||||
|
CHOP780214 Frequency of the 3rd residue in turn (Chou-Fasman, 1978b)
|
||||||
|
CHOP780215 Frequency of the 4th residue in turn (Chou-Fasman, 1978b)
|
||||||
|
CHOP780216 Normalized frequency of the 2nd and 3rd residues in turn (Chou-Fasman, 1978b)
|
||||||
|
CIDH920101 Normalized hydrophobicity scales for alpha-proteins (Cid et al., 1992)
|
||||||
|
CIDH920102 Normalized hydrophobicity scales for beta-proteins (Cid et al., 1992)
|
||||||
|
CIDH920103 Normalized hydrophobicity scales for alpha+beta-proteins (Cid et al., 1992)
|
||||||
|
CIDH920104 Normalized hydrophobicity scales for alpha/beta-proteins (Cid et al., 1992)
|
||||||
|
CIDH920105 Normalized average hydrophobicity scales (Cid et al., 1992)
|
||||||
|
COHE430101 Partial specific volume (Cohn-Edsall, 1943)
|
||||||
|
CRAJ730101 Normalized frequency of middle helix (Crawford et al., 1973)
|
||||||
|
CRAJ730102 Normalized frequency of beta-sheet (Crawford et al., 1973)
|
||||||
|
CRAJ730103 Normalized frequency of turn (Crawford et al., 1973)
|
||||||
|
DAWD720101 Size (Dawson, 1972)
|
||||||
|
DAYM780101 Amino acid composition (Dayhoff et al., 1978a)
|
||||||
|
DAYM780201 Relative mutability (Dayhoff et al., 1978b)
|
||||||
|
DESM900101 Membrane preference for cytochrome b: MPH89 (Degli Esposti et al., 1990)
|
||||||
|
DESM900102 Average membrane preference: AMP07 (Degli Esposti et al., 1990)
|
||||||
|
EISD840101 Consensus normalized hydrophobicity scale (Eisenberg, 1984)
|
||||||
|
EISD860101 Solvation free energy (Eisenberg-McLachlan, 1986)
|
||||||
|
EISD860102 Atom-based hydrophobic moment (Eisenberg-McLachlan, 1986)
|
||||||
|
EISD860103 Direction of hydrophobic moment (Eisenberg-McLachlan, 1986)
|
||||||
|
FASG760101 Molecular weight (Fasman, 1976)
|
||||||
|
FASG760102 Melting point (Fasman, 1976)
|
||||||
|
FASG760103 Optical rotation (Fasman, 1976)
|
||||||
|
FASG760104 pK-N (Fasman, 1976)
|
||||||
|
FASG760105 pK-C (Fasman, 1976)
|
||||||
|
FAUJ830101 Hydrophobic parameter pi (Fauchere-Pliska, 1983)
|
||||||
|
FAUJ880101 Graph shape index (Fauchere et al., 1988)
|
||||||
|
FAUJ880102 Smoothed upsilon steric parameter (Fauchere et al., 1988)
|
||||||
|
FAUJ880103 Normalized van der Waals volume (Fauchere et al., 1988)
|
||||||
|
FAUJ880104 STERIMOL length of the side chain (Fauchere et al., 1988)
|
||||||
|
FAUJ880105 STERIMOL minimum width of the side chain (Fauchere et al., 1988)
|
||||||
|
FAUJ880106 STERIMOL maximum width of the side chain (Fauchere et al., 1988)
|
||||||
|
FAUJ880107 N.m.r. chemical shift of alpha-carbon (Fauchere et al., 1988)
|
||||||
|
FAUJ880108 Localized electrical effect (Fauchere et al., 1988)
|
||||||
|
FAUJ880109 Number of hydrogen bond donors (Fauchere et al., 1988)
|
||||||
|
FAUJ880110 Number of full nonbonding orbitals (Fauchere et al., 1988)
|
||||||
|
FAUJ880111 Positive charge (Fauchere et al., 1988)
|
||||||
|
FAUJ880112 Negative charge (Fauchere et al., 1988)
|
||||||
|
FAUJ880113 pK-a(RCOOH) (Fauchere et al., 1988)
|
||||||
|
FINA770101 Helix-coil equilibrium constant (Finkelstein-Ptitsyn, 1977)
|
||||||
|
FINA910101 Helix initiation parameter at posision i-1 (Finkelstein et al., 1991)
|
||||||
|
FINA910102 Helix initiation parameter at posision i,i+1,i+2 (Finkelstein et al., 1991)
|
||||||
|
FINA910103 Helix termination parameter at posision j-2,j-1,j (Finkelstein et al., 1991)
|
||||||
|
FINA910104 Helix termination parameter at posision j+1 (Finkelstein et al., 1991)
|
||||||
|
GARJ730101 Partition coefficient (Garel et al., 1973)
|
||||||
|
GEIM800101 Alpha-helix indices (Geisow-Roberts, 1980)
|
||||||
|
GEIM800102 Alpha-helix indices for alpha-proteins (Geisow-Roberts, 1980)
|
||||||
|
GEIM800103 Alpha-helix indices for beta-proteins (Geisow-Roberts, 1980)
|
||||||
|
GEIM800104 Alpha-helix indices for alpha/beta-proteins (Geisow-Roberts, 1980)
|
||||||
|
GEIM800105 Beta-strand indices (Geisow-Roberts, 1980)
|
||||||
|
GEIM800106 Beta-strand indices for beta-proteins (Geisow-Roberts, 1980)
|
||||||
|
GEIM800107 Beta-strand indices for alpha/beta-proteins (Geisow-Roberts, 1980)
|
||||||
|
GEIM800108 Aperiodic indices (Geisow-Roberts, 1980)
|
||||||
|
GEIM800109 Aperiodic indices for alpha-proteins (Geisow-Roberts, 1980)
|
||||||
|
GEIM800110 Aperiodic indices for beta-proteins (Geisow-Roberts, 1980)
|
||||||
|
GEIM800111 Aperiodic indices for alpha/beta-proteins (Geisow-Roberts, 1980)
|
||||||
|
GOLD730101 Hydrophobicity factor (Goldsack-Chalifoux, 1973)
|
||||||
|
GOLD730102 Residue volume (Goldsack-Chalifoux, 1973)
|
||||||
|
GRAR740101 Composition (Grantham, 1974)
|
||||||
|
GRAR740102 Polarity (Grantham, 1974)
|
||||||
|
GRAR740103 Volume (Grantham, 1974)
|
||||||
|
GUYH850101 Partition energy (Guy, 1985)
|
||||||
|
HOPA770101 Hydration number (Hopfinger, 1971), Cited by Charton-Charton (1982)
|
||||||
|
HOPT810101 Hydrophilicity value (Hopp-Woods, 1981)
|
||||||
|
HUTJ700101 Heat capacity (Hutchens, 1970)
|
||||||
|
HUTJ700102 Absolute entropy (Hutchens, 1970)
|
||||||
|
HUTJ700103 Entropy of formation (Hutchens, 1970)
|
||||||
|
ISOY800101 Normalized relative frequency of alpha-helix (Isogai et al., 1980)
|
||||||
|
ISOY800102 Normalized relative frequency of extended structure (Isogai et al., 1980)
|
||||||
|
ISOY800103 Normalized relative frequency of bend (Isogai et al., 1980)
|
||||||
|
ISOY800104 Normalized relative frequency of bend R (Isogai et al., 1980)
|
||||||
|
ISOY800105 Normalized relative frequency of bend S (Isogai et al., 1980)
|
||||||
|
ISOY800106 Normalized relative frequency of helix end (Isogai et al., 1980)
|
||||||
|
ISOY800107 Normalized relative frequency of double bend (Isogai et al., 1980)
|
||||||
|
ISOY800108 Normalized relative frequency of coil (Isogai et al., 1980)
|
||||||
|
JANJ780101 Average accessible surface area (Janin et al., 1978)
|
||||||
|
JANJ780102 Percentage of buried residues (Janin et al., 1978)
|
||||||
|
JANJ780103 Percentage of exposed residues (Janin et al., 1978)
|
||||||
|
JANJ790101 Ratio of buried and accessible molar fractions (Janin, 1979)
|
||||||
|
JANJ790102 Transfer free energy (Janin, 1979)
|
||||||
|
JOND750101 Hydrophobicity (Jones, 1975)
|
||||||
|
JOND750102 pK (-COOH) (Jones, 1975)
|
||||||
|
JOND920101 Relative frequency of occurrence (Jones et al., 1992)
|
||||||
|
JOND920102 Relative mutability (Jones et al., 1992)
|
||||||
|
JUKT750101 Amino acid distribution (Jukes et al., 1975)
|
||||||
|
JUNJ780101 Sequence frequency (Jungck, 1978)
|
||||||
|
KANM800101 Average relative probability of helix (Kanehisa-Tsong, 1980)
|
||||||
|
KANM800102 Average relative probability of beta-sheet (Kanehisa-Tsong, 1980)
|
||||||
|
KANM800103 Average relative probability of inner helix (Kanehisa-Tsong, 1980)
|
||||||
|
KANM800104 Average relative probability of inner beta-sheet (Kanehisa-Tsong, 1980)
|
||||||
|
KARP850101 Flexibility parameter for no rigid neighbors (Karplus-Schulz, 1985)
|
||||||
|
KARP850102 Flexibility parameter for one rigid neighbor (Karplus-Schulz, 1985)
|
||||||
|
KARP850103 Flexibility parameter for two rigid neighbors (Karplus-Schulz, 1985)
|
||||||
|
KHAG800101 The Kerr-constant increments (Khanarian-Moore, 1980)
|
||||||
|
KLEP840101 Net charge (Klein et al., 1984)
|
||||||
|
KRIW710101 Side chain interaction parameter (Krigbaum-Rubin, 1971)
|
||||||
|
KRIW790101 Side chain interaction parameter (Krigbaum-Komoriya, 1979)
|
||||||
|
KRIW790102 Fraction of site occupied by water (Krigbaum-Komoriya, 1979)
|
||||||
|
KRIW790103 Side chain volume (Krigbaum-Komoriya, 1979)
|
||||||
|
KYTJ820101 Hydropathy index (Kyte-Doolittle, 1982)
|
||||||
|
LAWE840101 Transfer free energy, CHP/water (Lawson et al., 1984)
|
||||||
|
LEVM760101 Hydrophobic parameter (Levitt, 1976)
|
||||||
|
LEVM760102 Distance between C-alpha and centroid of side chain (Levitt, 1976)
|
||||||
|
LEVM760103 Side chain angle theta(AAR) (Levitt, 1976)
|
||||||
|
LEVM760104 Side chain torsion angle phi(AAAR) (Levitt, 1976)
|
||||||
|
LEVM760105 Radius of gyration of side chain (Levitt, 1976)
|
||||||
|
LEVM760106 van der Waals parameter R0 (Levitt, 1976)
|
||||||
|
LEVM760107 van der Waals parameter epsilon (Levitt, 1976)
|
||||||
|
LEVM780101 Normalized frequency of alpha-helix, with weights (Levitt, 1978)
|
||||||
|
LEVM780102 Normalized frequency of beta-sheet, with weights (Levitt, 1978)
|
||||||
|
LEVM780103 Normalized frequency of reverse turn, with weights (Levitt, 1978)
|
||||||
|
LEVM780104 Normalized frequency of alpha-helix, unweighted (Levitt, 1978)
|
||||||
|
LEVM780105 Normalized frequency of beta-sheet, unweighted (Levitt, 1978)
|
||||||
|
LEVM780106 Normalized frequency of reverse turn, unweighted (Levitt, 1978)
|
||||||
|
LEWP710101 Frequency of occurrence in beta-bends (Lewis et al., 1971)
|
||||||
|
LIFS790101 Conformational preference for all beta-strands (Lifson-Sander, 1979)
|
||||||
|
LIFS790102 Conformational preference for parallel beta-strands (Lifson-Sander, 1979)
|
||||||
|
LIFS790103 Conformational preference for antiparallel beta-strands (Lifson-Sander, 1979)
|
||||||
|
MANP780101 Average surrounding hydrophobicity (Manavalan-Ponnuswamy, 1978)
|
||||||
|
MAXF760101 Normalized frequency of alpha-helix (Maxfield-Scheraga, 1976)
|
||||||
|
MAXF760102 Normalized frequency of extended structure (Maxfield-Scheraga, 1976)
|
||||||
|
MAXF760103 Normalized frequency of zeta R (Maxfield-Scheraga, 1976)
|
||||||
|
MAXF760104 Normalized frequency of left-handed alpha-helix (Maxfield-Scheraga, 1976)
|
||||||
|
MAXF760105 Normalized frequency of zeta L (Maxfield-Scheraga, 1976)
|
||||||
|
MAXF760106 Normalized frequency of alpha region (Maxfield-Scheraga, 1976)
|
||||||
|
MCMT640101 Refractivity (McMeekin et al., 1964), Cited by Jones (1975)
|
||||||
|
MEEJ800101 Retention coefficient in HPLC, pH7.4 (Meek, 1980)
|
||||||
|
MEEJ800102 Retention coefficient in HPLC, pH2.1 (Meek, 1980)
|
||||||
|
MEEJ810101 Retention coefficient in NaClO4 (Meek-Rossetti, 1981)
|
||||||
|
MEEJ810102 Retention coefficient in NaH2PO4 (Meek-Rossetti, 1981)
|
||||||
|
MEIH800101 Average reduced distance for C-alpha (Meirovitch et al., 1980)
|
||||||
|
MEIH800102 Average reduced distance for side chain (Meirovitch et al., 1980)
|
||||||
|
MEIH800103 Average side chain orientation angle (Meirovitch et al., 1980)
|
||||||
|
MIYS850101 Effective partition energy (Miyazawa-Jernigan, 1985)
|
||||||
|
NAGK730101 Normalized frequency of alpha-helix (Nagano, 1973)
|
||||||
|
NAGK730102 Normalized frequency of bata-structure (Nagano, 1973)
|
||||||
|
NAGK730103 Normalized frequency of coil (Nagano, 1973)
|
||||||
|
NAKH900101 AA composition of total proteins (Nakashima et al., 1990)
|
||||||
|
NAKH900102 SD of AA composition of total proteins (Nakashima et al., 1990)
|
||||||
|
NAKH900103 AA composition of mt-proteins (Nakashima et al., 1990)
|
||||||
|
NAKH900104 Normalized composition of mt-proteins (Nakashima et al., 1990)
|
||||||
|
NAKH900105 AA composition of mt-proteins from animal (Nakashima et al., 1990)
|
||||||
|
NAKH900106 Normalized composition from animal (Nakashima et al., 1990)
|
||||||
|
NAKH900107 AA composition of mt-proteins from fungi and plant (Nakashima et al., 1990)
|
||||||
|
NAKH900108 Normalized composition from fungi and plant (Nakashima et al., 1990)
|
||||||
|
NAKH900109 AA composition of membrane proteins (Nakashima et al., 1990)
|
||||||
|
NAKH900110 Normalized composition of membrane proteins (Nakashima et al., 1990)
|
||||||
|
NAKH900111 Transmembrane regions of non-mt-proteins (Nakashima et al., 1990)
|
||||||
|
NAKH900112 Transmembrane regions of mt-proteins (Nakashima et al., 1990)
|
||||||
|
NAKH900113 Ratio of average and computed composition (Nakashima et al., 1990)
|
||||||
|
NAKH920101 AA composition of CYT of single-spanning proteins (Nakashima-Nishikawa, 1992)
|
||||||
|
NAKH920102 AA composition of CYT2 of single-spanning proteins (Nakashima-Nishikawa, 1992)
|
||||||
|
NAKH920103 AA composition of EXT of single-spanning proteins (Nakashima-Nishikawa, 1992)
|
||||||
|
NAKH920104 AA composition of EXT2 of single-spanning proteins (Nakashima-Nishikawa, 1992)
|
||||||
|
NAKH920105 AA composition of MEM of single-spanning proteins (Nakashima-Nishikawa, 1992)
|
||||||
|
NAKH920106 AA composition of CYT of multi-spanning proteins (Nakashima-Nishikawa, 1992)
|
||||||
|
NAKH920107 AA composition of EXT of multi-spanning proteins (Nakashima-Nishikawa, 1992)
|
||||||
|
NAKH920108 AA composition of MEM of multi-spanning proteins (Nakashima-Nishikawa, 1992)
|
||||||
|
NISK800101 8 A contact number (Nishikawa-Ooi, 1980)
|
||||||
|
NISK860101 14 A contact number (Nishikawa-Ooi, 1986)
|
||||||
|
NOZY710101 Transfer energy, organic solvent/water (Nozaki-Tanford, 1971)
|
||||||
|
OOBM770101 Average non-bonded energy per atom (Oobatake-Ooi, 1977)
|
||||||
|
OOBM770102 Short and medium range non-bonded energy per atom (Oobatake-Ooi, 1977)
|
||||||
|
OOBM770103 Long range non-bonded energy per atom (Oobatake-Ooi, 1977)
|
||||||
|
OOBM770104 Average non-bonded energy per residue (Oobatake-Ooi, 1977)
|
||||||
|
OOBM770105 Short and medium range non-bonded energy per residue (Oobatake-Ooi, 1977)
|
||||||
|
OOBM850101 Optimized beta-structure-coil equilibrium constant (Oobatake et al., 1985)
|
||||||
|
OOBM850102 Optimized propensity to form reverse turn (Oobatake et al., 1985)
|
||||||
|
OOBM850103 Optimized transfer energy parameter (Oobatake et al., 1985)
|
||||||
|
OOBM850104 Optimized average non-bonded energy per atom (Oobatake et al., 1985)
|
||||||
|
OOBM850105 Optimized side chain interaction parameter (Oobatake et al., 1985)
|
||||||
|
PALJ810101 Normalized frequency of alpha-helix from LG (Palau et al., 1981)
|
||||||
|
PALJ810102 Normalized frequency of alpha-helix from CF (Palau et al., 1981)
|
||||||
|
PALJ810103 Normalized frequency of beta-sheet from LG (Palau et al., 1981)
|
||||||
|
PALJ810104 Normalized frequency of beta-sheet from CF (Palau et al., 1981)
|
||||||
|
PALJ810105 Normalized frequency of turn from LG (Palau et al., 1981)
|
||||||
|
PALJ810106 Normalized frequency of turn from CF (Palau et al., 1981)
|
||||||
|
PALJ810107 Normalized frequency of alpha-helix in all-alpha class (Palau et al., 1981)
|
||||||
|
PALJ810108 Normalized frequency of alpha-helix in alpha+beta class (Palau et al., 1981)
|
||||||
|
PALJ810109 Normalized frequency of alpha-helix in alpha/beta class (Palau et al., 1981)
|
||||||
|
PALJ810110 Normalized frequency of beta-sheet in all-beta class (Palau et al., 1981)
|
||||||
|
PALJ810111 Normalized frequency of beta-sheet in alpha+beta class (Palau et al., 1981)
|
||||||
|
PALJ810112 Normalized frequency of beta-sheet in alpha/beta class (Palau et al., 1981)
|
||||||
|
PALJ810113 Normalized frequency of turn in all-alpha class (Palau et al., 1981)
|
||||||
|
PALJ810114 Normalized frequency of turn in all-beta class (Palau et al., 1981)
|
||||||
|
PALJ810115 Normalized frequency of turn in alpha+beta class (Palau et al., 1981)
|
||||||
|
PALJ810116 Normalized frequency of turn in alpha/beta class (Palau et al., 1981)
|
||||||
|
PARJ860101 HPLC parameter (Parker et al., 1986)
|
||||||
|
PLIV810101 Partition coefficient (Pliska et al., 1981)
|
||||||
|
PONP800101 Surrounding hydrophobicity in folded form (Ponnuswamy et al., 1980)
|
||||||
|
PONP800102 Average gain in surrounding hydrophobicity (Ponnuswamy et al., 1980)
|
||||||
|
PONP800103 Average gain ratio in surrounding hydrophobicity (Ponnuswamy et al., 1980)
|
||||||
|
PONP800104 Surrounding hydrophobicity in alpha-helix (Ponnuswamy et al., 1980)
|
||||||
|
PONP800105 Surrounding hydrophobicity in beta-sheet (Ponnuswamy et al., 1980)
|
||||||
|
PONP800106 Surrounding hydrophobicity in turn (Ponnuswamy et al., 1980)
|
||||||
|
PONP800107 Accessibility reduction ratio (Ponnuswamy et al., 1980)
|
||||||
|
PONP800108 Average number of surrounding residues (Ponnuswamy et al., 1980)
|
||||||
|
PRAM820101 Intercept in regression analysis (Prabhakaran-Ponnuswamy, 1982)
|
||||||
|
PRAM820102 Slope in regression analysis x 1.0E1 (Prabhakaran-Ponnuswamy, 1982)
|
||||||
|
PRAM820103 Correlation coefficient in regression analysis (Prabhakaran-Ponnuswamy, 1982)
|
||||||
|
PRAM900101 Hydrophobicity (Prabhakaran, 1990)
|
||||||
|
PRAM900102 Relative frequency in alpha-helix (Prabhakaran, 1990)
|
||||||
|
PRAM900103 Relative frequency in beta-sheet (Prabhakaran, 1990)
|
||||||
|
PRAM900104 Relative frequency in reverse-turn (Prabhakaran, 1990)
|
||||||
|
PTIO830101 Helix-coil equilibrium constant (Ptitsyn-Finkelstein, 1983)
|
||||||
|
PTIO830102 Beta-coil equilibrium constant (Ptitsyn-Finkelstein, 1983)
|
||||||
|
QIAN880101 Weights for alpha-helix at the window position of -6 (Qian-Sejnowski, 1988)
|
||||||
|
QIAN880102 Weights for alpha-helix at the window position of -5 (Qian-Sejnowski, 1988)
|
||||||
|
QIAN880103 Weights for alpha-helix at the window position of -4 (Qian-Sejnowski, 1988)
|
||||||
|
QIAN880104 Weights for alpha-helix at the window position of -3 (Qian-Sejnowski, 1988)
|
||||||
|
QIAN880105 Weights for alpha-helix at the window position of -2 (Qian-Sejnowski, 1988)
|
||||||
|
QIAN880106 Weights for alpha-helix at the window position of -1 (Qian-Sejnowski, 1988)
|
||||||
|
QIAN880107 Weights for alpha-helix at the window position of 0 (Qian-Sejnowski, 1988)
|
||||||
|
QIAN880108 Weights for alpha-helix at the window position of 1 (Qian-Sejnowski, 1988)
|
||||||
|
QIAN880109 Weights for alpha-helix at the window position of 2 (Qian-Sejnowski, 1988)
|
||||||
|
QIAN880110 Weights for alpha-helix at the window position of 3 (Qian-Sejnowski, 1988)
|
||||||
|
QIAN880111 Weights for alpha-helix at the window position of 4 (Qian-Sejnowski, 1988)
|
||||||
|
QIAN880112 Weights for alpha-helix at the window position of 5 (Qian-Sejnowski, 1988)
|
||||||
|
QIAN880113 Weights for alpha-helix at the window position of 6 (Qian-Sejnowski, 1988)
|
||||||
|
QIAN880114 Weights for beta-sheet at the window position of -6 (Qian-Sejnowski, 1988)
|
||||||
|
QIAN880115 Weights for beta-sheet at the window position of -5 (Qian-Sejnowski, 1988)
|
||||||
|
QIAN880116 Weights for beta-sheet at the window position of -4 (Qian-Sejnowski, 1988)
|
||||||
|
QIAN880117 Weights for beta-sheet at the window position of -3 (Qian-Sejnowski, 1988)
|
||||||
|
QIAN880118 Weights for beta-sheet at the window position of -2 (Qian-Sejnowski, 1988)
|
||||||
|
QIAN880119 Weights for beta-sheet at the window position of -1 (Qian-Sejnowski, 1988)
|
||||||
|
QIAN880120 Weights for beta-sheet at the window position of 0 (Qian-Sejnowski, 1988)
|
||||||
|
QIAN880121 Weights for beta-sheet at the window position of 1 (Qian-Sejnowski, 1988)
|
||||||
|
QIAN880122 Weights for beta-sheet at the window position of 2 (Qian-Sejnowski, 1988)
|
||||||
|
QIAN880123 Weights for beta-sheet at the window position of 3 (Qian-Sejnowski, 1988)
|
||||||
|
QIAN880124 Weights for beta-sheet at the window position of 4 (Qian-Sejnowski, 1988)
|
||||||
|
QIAN880125 Weights for beta-sheet at the window position of 5 (Qian-Sejnowski, 1988)
|
||||||
|
QIAN880126 Weights for beta-sheet at the window position of 6 (Qian-Sejnowski, 1988)
|
||||||
|
QIAN880127 Weights for coil at the window position of -6 (Qian-Sejnowski, 1988)
|
||||||
|
QIAN880128 Weights for coil at the window position of -5 (Qian-Sejnowski, 1988)
|
||||||
|
QIAN880129 Weights for coil at the window position of -4 (Qian-Sejnowski, 1988)
|
||||||
|
QIAN880130 Weights for coil at the window position of -3 (Qian-Sejnowski, 1988)
|
||||||
|
QIAN880131 Weights for coil at the window position of -2 (Qian-Sejnowski, 1988)
|
||||||
|
QIAN880132 Weights for coil at the window position of -1 (Qian-Sejnowski, 1988)
|
||||||
|
QIAN880133 Weights for coil at the window position of 0 (Qian-Sejnowski, 1988)
|
||||||
|
QIAN880134 Weights for coil at the window position of 1 (Qian-Sejnowski, 1988)
|
||||||
|
QIAN880135 Weights for coil at the window position of 2 (Qian-Sejnowski, 1988)
|
||||||
|
QIAN880136 Weights for coil at the window position of 3 (Qian-Sejnowski, 1988)
|
||||||
|
QIAN880137 Weights for coil at the window position of 4 (Qian-Sejnowski, 1988)
|
||||||
|
QIAN880138 Weights for coil at the window position of 5 (Qian-Sejnowski, 1988)
|
||||||
|
QIAN880139 Weights for coil at the window position of 6 (Qian-Sejnowski, 1988)
|
||||||
|
RACS770101 Average reduced distance for C-alpha (Rackovsky-Scheraga, 1977)
|
||||||
|
RACS770102 Average reduced distance for side chain (Rackovsky-Scheraga, 1977)
|
||||||
|
RACS770103 Side chain orientational preference (Rackovsky-Scheraga, 1977)
|
||||||
|
RACS820101 Average relative fractional occurrence in A0(i) (Rackovsky-Scheraga, 1982)
|
||||||
|
RACS820102 Average relative fractional occurrence in AR(i) (Rackovsky-Scheraga, 1982)
|
||||||
|
RACS820103 Average relative fractional occurrence in AL(i) (Rackovsky-Scheraga, 1982)
|
||||||
|
RACS820104 Average relative fractional occurrence in EL(i) (Rackovsky-Scheraga, 1982)
|
||||||
|
RACS820105 Average relative fractional occurrence in E0(i) (Rackovsky-Scheraga, 1982)
|
||||||
|
RACS820106 Average relative fractional occurrence in ER(i) (Rackovsky-Scheraga, 1982)
|
||||||
|
RACS820107 Average relative fractional occurrence in A0(i-1) (Rackovsky-Scheraga, 1982)
|
||||||
|
RACS820108 Average relative fractional occurrence in AR(i-1) (Rackovsky-Scheraga, 1982)
|
||||||
|
RACS820109 Average relative fractional occurrence in AL(i-1) (Rackovsky-Scheraga, 1982)
|
||||||
|
RACS820110 Average relative fractional occurrence in EL(i-1) (Rackovsky-Scheraga, 1982)
|
||||||
|
RACS820111 Average relative fractional occurrence in E0(i-1) (Rackovsky-Scheraga, 1982)
|
||||||
|
RACS820112 Average relative fractional occurrence in ER(i-1) (Rackovsky-Scheraga, 1982)
|
||||||
|
RACS820113 Value of theta(i) (Rackovsky-Scheraga, 1982)
|
||||||
|
RACS820114 Value of theta(i-1) (Rackovsky-Scheraga, 1982)
|
||||||
|
RADA880101 Transfer free energy from chx to wat (Radzicka-Wolfenden, 1988)
|
||||||
|
RADA880102 Transfer free energy from oct to wat (Radzicka-Wolfenden, 1988)
|
||||||
|
RADA880103 Transfer free energy from vap to chx (Radzicka-Wolfenden, 1988)
|
||||||
|
RADA880104 Transfer free energy from chx to oct (Radzicka-Wolfenden, 1988)
|
||||||
|
RADA880105 Transfer free energy from vap to oct (Radzicka-Wolfenden, 1988)
|
||||||
|
RADA880106 Accessible surface area (Radzicka-Wolfenden, 1988)
|
||||||
|
RADA880107 Energy transfer from out to in(95%buried) (Radzicka-Wolfenden, 1988)
|
||||||
|
RADA880108 Mean polarity (Radzicka-Wolfenden, 1988)
|
||||||
|
RICJ880101 Relative preference value at N" (Richardson-Richardson, 1988)
|
||||||
|
RICJ880102 Relative preference value at N' (Richardson-Richardson, 1988)
|
||||||
|
RICJ880103 Relative preference value at N-cap (Richardson-Richardson, 1988)
|
||||||
|
RICJ880104 Relative preference value at N1 (Richardson-Richardson, 1988)
|
||||||
|
RICJ880105 Relative preference value at N2 (Richardson-Richardson, 1988)
|
||||||
|
RICJ880106 Relative preference value at N3 (Richardson-Richardson, 1988)
|
||||||
|
RICJ880107 Relative preference value at N4 (Richardson-Richardson, 1988)
|
||||||
|
RICJ880108 Relative preference value at N5 (Richardson-Richardson, 1988)
|
||||||
|
RICJ880109 Relative preference value at Mid (Richardson-Richardson, 1988)
|
||||||
|
RICJ880110 Relative preference value at C5 (Richardson-Richardson, 1988)
|
||||||
|
RICJ880111 Relative preference value at C4 (Richardson-Richardson, 1988)
|
||||||
|
RICJ880112 Relative preference value at C3 (Richardson-Richardson, 1988)
|
||||||
|
RICJ880113 Relative preference value at C2 (Richardson-Richardson, 1988)
|
||||||
|
RICJ880114 Relative preference value at C1 (Richardson-Richardson, 1988)
|
||||||
|
RICJ880115 Relative preference value at C-cap (Richardson-Richardson, 1988)
|
||||||
|
RICJ880116 Relative preference value at C' (Richardson-Richardson, 1988)
|
||||||
|
RICJ880117 Relative preference value at C" (Richardson-Richardson, 1988)
|
||||||
|
ROBB760101 Information measure for alpha-helix (Robson-Suzuki, 1976)
|
||||||
|
ROBB760102 Information measure for N-terminal helix (Robson-Suzuki, 1976)
|
||||||
|
ROBB760103 Information measure for middle helix (Robson-Suzuki, 1976)
|
||||||
|
ROBB760104 Information measure for C-terminal helix (Robson-Suzuki, 1976)
|
||||||
|
ROBB760105 Information measure for extended (Robson-Suzuki, 1976)
|
||||||
|
ROBB760106 Information measure for pleated-sheet (Robson-Suzuki, 1976)
|
||||||
|
ROBB760107 Information measure for extended without H-bond (Robson-Suzuki, 1976)
|
||||||
|
ROBB760108 Information measure for turn (Robson-Suzuki, 1976)
|
||||||
|
ROBB760109 Information measure for N-terminal turn (Robson-Suzuki, 1976)
|
||||||
|
ROBB760110 Information measure for middle turn (Robson-Suzuki, 1976)
|
||||||
|
ROBB760111 Information measure for C-terminal turn (Robson-Suzuki, 1976)
|
||||||
|
ROBB760112 Information measure for coil (Robson-Suzuki, 1976)
|
||||||
|
ROBB760113 Information measure for loop (Robson-Suzuki, 1976)
|
||||||
|
ROBB790101 Hydration free energy (Robson-Osguthorpe, 1979)
|
||||||
|
ROSG850101 Mean area buried on transfer (Rose et al., 1985)
|
||||||
|
ROSG850102 Mean fractional area loss (Rose et al., 1985)
|
||||||
|
ROSM880101 Side chain hydropathy, uncorrected for solvation (Roseman, 1988)
|
||||||
|
ROSM880102 Side chain hydropathy, corrected for solvation (Roseman, 1988)
|
||||||
|
ROSM880103 Loss of Side chain hydropathy by helix formation (Roseman, 1988)
|
||||||
|
SIMZ760101 Transfer free energy (Simon, 1976), Cited by Charton-Charton (1982)
|
||||||
|
SNEP660101 Principal component I (Sneath, 1966)
|
||||||
|
SNEP660102 Principal component II (Sneath, 1966)
|
||||||
|
SNEP660103 Principal component III (Sneath, 1966)
|
||||||
|
SNEP660104 Principal component IV (Sneath, 1966)
|
||||||
|
SUEM840101 Zimm-Bragg parameter s at 20 C (Sueki et al., 1984)
|
||||||
|
SUEM840102 Zimm-Bragg parameter sigma x 1.0E4 (Sueki et al., 1984)
|
||||||
|
SWER830101 Optimal matching hydrophobicity (Sweet-Eisenberg, 1983)
|
||||||
|
TANS770101 Normalized frequency of alpha-helix (Tanaka-Scheraga, 1977)
|
||||||
|
TANS770102 Normalized frequency of isolated helix (Tanaka-Scheraga, 1977)
|
||||||
|
TANS770103 Normalized frequency of extended structure (Tanaka-Scheraga, 1977)
|
||||||
|
TANS770104 Normalized frequency of chain reversal R (Tanaka-Scheraga, 1977)
|
||||||
|
TANS770105 Normalized frequency of chain reversal S (Tanaka-Scheraga, 1977)
|
||||||
|
TANS770106 Normalized frequency of chain reversal D (Tanaka-Scheraga, 1977)
|
||||||
|
TANS770107 Normalized frequency of left-handed helix (Tanaka-Scheraga, 1977)
|
||||||
|
TANS770108 Normalized frequency of zeta R (Tanaka-Scheraga, 1977)
|
||||||
|
TANS770109 Normalized frequency of coil (Tanaka-Scheraga, 1977)
|
||||||
|
TANS770110 Normalized frequency of chain reversal (Tanaka-Scheraga, 1977)
|
||||||
|
VASM830101 Relative population of conformational state A (Vasquez et al., 1983)
|
||||||
|
VASM830102 Relative population of conformational state C (Vasquez et al., 1983)
|
||||||
|
VASM830103 Relative population of conformational state E (Vasquez et al., 1983)
|
||||||
|
VELV850101 Electron-ion interaction potential (Veljkovic et al., 1985)
|
||||||
|
VENT840101 Bitterness (Venanzi, 1984)
|
||||||
|
VHEG790101 Transfer free energy to lipophilic phase (von Heijne-Blomberg, 1979)
|
||||||
|
WARP780101 Average interactions per side chain atom (Warme-Morgan, 1978)
|
||||||
|
WEBA780101 RF value in high salt chromatography (Weber-Lacey, 1978)
|
||||||
|
WERD780101 Propensity to be buried inside (Wertz-Scheraga, 1978)
|
||||||
|
WERD780102 Free energy change of epsilon(i) to epsilon(ex) (Wertz-Scheraga, 1978)
|
||||||
|
WERD780103 Free energy change of alpha(Ri) to alpha(Rh) (Wertz-Scheraga, 1978)
|
||||||
|
WERD780104 Free energy change of epsilon(i) to alpha(Rh) (Wertz-Scheraga, 1978)
|
||||||
|
WOEC730101 Polar requirement (Woese, 1973)
|
||||||
|
WOLR810101 Hydration potential (Wolfenden et al., 1981)
|
||||||
|
WOLS870101 Principal property value z1 (Wold et al., 1987)
|
||||||
|
WOLS870102 Principal property value z2 (Wold et al., 1987)
|
||||||
|
WOLS870103 Principal property value z3 (Wold et al., 1987)
|
||||||
|
YUTK870101 Unfolding Gibbs energy in water, pH7.0 (Yutani et al., 1987)
|
||||||
|
YUTK870102 Unfolding Gibbs energy in water, pH9.0 (Yutani et al., 1987)
|
||||||
|
YUTK870103 Activation Gibbs energy of unfolding, pH7.0 (Yutani et al., 1987)
|
||||||
|
YUTK870104 Activation Gibbs energy of unfolding, pH9.0 (Yutani et al., 1987)
|
||||||
|
ZASB820101 Dependence of partition coefficient on ionic strength (Zaslavsky et al., 1982)
|
||||||
|
ZIMJ680101 Hydrophobicity (Zimmerman et al., 1968)
|
||||||
|
ZIMJ680102 Bulkiness (Zimmerman et al., 1968)
|
||||||
|
ZIMJ680103 Polarity (Zimmerman et al., 1968)
|
||||||
|
ZIMJ680104 Isoelectric point (Zimmerman et al., 1968)
|
||||||
|
ZIMJ680105 RF rank (Zimmerman et al., 1968)
|
||||||
|
AURR980101 Normalized positional residue frequency at helix termini N4'(Aurora-Rose, 1998)
|
||||||
|
AURR980102 Normalized positional residue frequency at helix termini N"' (Aurora-Rose, 1998)
|
||||||
|
AURR980103 Normalized positional residue frequency at helix termini N" (Aurora-Rose, 1998)
|
||||||
|
AURR980104 Normalized positional residue frequency at helix termini N'(Aurora-Rose, 1998)
|
||||||
|
AURR980105 Normalized positional residue frequency at helix termini Nc (Aurora-Rose, 1998)
|
||||||
|
AURR980106 Normalized positional residue frequency at helix termini N1 (Aurora-Rose, 1998)
|
||||||
|
AURR980107 Normalized positional residue frequency at helix termini N2 (Aurora-Rose, 1998)
|
||||||
|
AURR980108 Normalized positional residue frequency at helix termini N3 (Aurora-Rose, 1998)
|
||||||
|
AURR980109 Normalized positional residue frequency at helix termini N4 (Aurora-Rose, 1998)
|
||||||
|
AURR980110 Normalized positional residue frequency at helix termini N5 (Aurora-Rose, 1998)
|
||||||
|
AURR980111 Normalized positional residue frequency at helix termini C5 (Aurora-Rose, 1998)
|
||||||
|
AURR980112 Normalized positional residue frequency at helix termini C4 (Aurora-Rose, 1998)
|
||||||
|
AURR980113 Normalized positional residue frequency at helix termini C3 (Aurora-Rose, 1998)
|
||||||
|
AURR980114 Normalized positional residue frequency at helix termini C2 (Aurora-Rose, 1998)
|
||||||
|
AURR980115 Normalized positional residue frequency at helix termini C1 (Aurora-Rose, 1998)
|
||||||
|
AURR980116 Normalized positional residue frequency at helix termini Cc (Aurora-Rose, 1998)
|
||||||
|
AURR980117 Normalized positional residue frequency at helix termini C' (Aurora-Rose, 1998)
|
||||||
|
AURR980118 Normalized positional residue frequency at helix termini C" (Aurora-Rose, 1998)
|
||||||
|
AURR980119 Normalized positional residue frequency at helix termini C"' (Aurora-Rose, 1998)
|
||||||
|
AURR980120 Normalized positional residue frequency at helix termini C4' (Aurora-Rose, 1998)
|
||||||
|
ONEK900101 Delta G values for the peptides extrapolated to 0 M urea (O'Neil-DeGrado, 1990)
|
||||||
|
ONEK900102 Helix formation parameters (delta delta G) (O'Neil-DeGrado, 1990)
|
||||||
|
VINM940101 Normalized flexibility parameters (B-values), average (Vihinen et al., 1994)
|
||||||
|
VINM940102 Normalized flexibility parameters (B-values) for each residue surrounded by none rigid neighbours (Vihinen et al., 1994)
|
||||||
|
VINM940103 Normalized flexibility parameters (B-values) for each residue surrounded by one rigid neighbours (Vihinen et al., 1994)
|
||||||
|
VINM940104 Normalized flexibility parameters (B-values) for each residue surrounded by two rigid neighbours (Vihinen et al., 1994)
|
||||||
|
MUNV940101 Free energy in alpha-helical conformation (Munoz-Serrano, 1994)
|
||||||
|
MUNV940102 Free energy in alpha-helical region (Munoz-Serrano, 1994)
|
||||||
|
MUNV940103 Free energy in beta-strand conformation (Munoz-Serrano, 1994)
|
||||||
|
MUNV940104 Free energy in beta-strand region (Munoz-Serrano, 1994)
|
||||||
|
MUNV940105 Free energy in beta-strand region (Munoz-Serrano, 1994)
|
||||||
|
WIMW960101 Free energies of transfer of AcWl-X-LL peptides from bilayer interface to water (Wimley-White, 1996)
|
||||||
|
KIMC930101 Thermodynamic beta sheet propensity (Kim-Berg, 1993)
|
||||||
|
MONM990101 Turn propensity scale for transmembrane helices (Monne et al., 1999)
|
||||||
|
BLAM930101 Alpha helix propensity of position 44 in T4 lysozyme (Blaber et al., 1993)
|
||||||
|
PARS000101 p-Values of mesophilic proteins based on the distributions of B values (Parthasarathy-Murthy, 2000)
|
||||||
|
PARS000102 p-Values of thermophilic proteins based on the distributions of B values (Parthasarathy-Murthy, 2000)
|
||||||
|
KUMS000101 Distribution of amino acid residues in the 18 non-redundant families of thermophilic proteins (Kumar et al., 2000)
|
||||||
|
KUMS000102 Distribution of amino acid residues in the 18 non-redundant families of mesophilic proteins (Kumar et al., 2000)
|
||||||
|
KUMS000103 Distribution of amino acid residues in the alpha-helices in thermophilic proteins (Kumar et al., 2000)
|
||||||
|
KUMS000104 Distribution of amino acid residues in the alpha-helices in mesophilic proteins (Kumar et al., 2000)
|
||||||
|
TAKK010101 Side-chain contribution to protein stability (kJ/mol) (Takano-Yutani, 2001)
|
||||||
|
FODM020101 Propensity of amino acids within pi-helices (Fodje-Al-Karadaghi, 2002)
|
||||||
|
NADH010101 Hydropathy scale based on self-information values in the two-state model (5% accessibility) (Naderi-Manesh et al., 2001)
|
||||||
|
NADH010102 Hydropathy scale based on self-information values in the two-state model (9% accessibility) (Naderi-Manesh et al., 2001)
|
||||||
|
NADH010103 Hydropathy scale based on self-information values in the two-state model (16% accessibility) (Naderi-Manesh et al., 2001)
|
||||||
|
NADH010104 Hydropathy scale based on self-information values in the two-state model (20% accessibility) (Naderi-Manesh et al., 2001)
|
||||||
|
NADH010105 Hydropathy scale based on self-information values in the two-state model (25% accessibility) (Naderi-Manesh et al., 2001)
|
||||||
|
NADH010106 Hydropathy scale based on self-information values in the two-state model (36% accessibility) (Naderi-Manesh et al., 2001)
|
||||||
|
NADH010107 Hydropathy scale based on self-information values in the two-state model (50% accessibility) (Naderi-Manesh et al., 2001)
|
||||||
|
MONM990201 Averaged turn propensities in a transmembrane helix (Monne et al., 1999)
|
||||||
|
KOEP990101 Alpha-helix propensity derived from designed sequences (Koehl-Levitt, 1999)
|
||||||
|
KOEP990102 Beta-sheet propensity derived from designed sequences (Koehl-Levitt, 1999)
|
||||||
|
CEDJ970101 Composition of amino acids in extracellular proteins (percent) (Cedano et al., 1997)
|
||||||
|
CEDJ970102 Composition of amino acids in anchored proteins (percent) (Cedano et al., 1997)
|
||||||
|
CEDJ970103 Composition of amino acids in membrane proteins (percent) (Cedano et al., 1997)
|
||||||
|
CEDJ970104 Composition of amino acids in intracellular proteins (percent) (Cedano et al., 1997)
|
||||||
|
CEDJ970105 Composition of amino acids in nuclear proteins (percent) (Cedano et al., 1997)
|
||||||
|
FUKS010101 Surface composition of amino acids in intracellular proteins of thermophiles (percent) (Fukuchi-Nishikawa, 2001)
|
||||||
|
FUKS010102 Surface composition of amino acids in intracellular proteins of mesophiles (percent) (Fukuchi-Nishikawa, 2001)
|
||||||
|
FUKS010103 Surface composition of amino acids in extracellular proteins of mesophiles (percent) (Fukuchi-Nishikawa, 2001)
|
||||||
|
FUKS010104 Surface composition of amino acids in nuclear proteins (percent) (Fukuchi-Nishikawa, 2001)
|
||||||
|
FUKS010105 Interior composition of amino acids in intracellular proteins of thermophiles (percent) (Fukuchi-Nishikawa, 2001)
|
||||||
|
FUKS010106 Interior composition of amino acids in intracellular proteins of mesophiles (percent) (Fukuchi-Nishikawa, 2001)
|
||||||
|
FUKS010107 Interior composition of amino acids in extracellular proteins of mesophiles (percent) (Fukuchi-Nishikawa, 2001)
|
||||||
|
FUKS010108 Interior composition of amino acids in nuclear proteins (percent) (Fukuchi-Nishikawa, 2001)
|
||||||
|
FUKS010109 Entire chain composition of amino acids in intracellular proteins of thermophiles (percent) (Fukuchi-Nishikawa, 2001)
|
||||||
|
FUKS010110 Entire chain composition of amino acids in intracellular proteins of mesophiles (percent) (Fukuchi-Nishikawa, 2001)
|
||||||
|
FUKS010111 Entire chain composition of amino acids in extracellular proteins of mesophiles (percent) (Fukuchi-Nishikawa, 2001)
|
||||||
|
FUKS010112 Entire chain compositino of amino acids in nuclear proteins (percent) (Fukuchi-Nishikawa, 2001)
|
||||||
|
AVBF000101 Screening coefficients gamma, local (Avbelj, 2000)
|
||||||
|
AVBF000102 Screening coefficients gamma, non-local (Avbelj, 2000)
|
||||||
|
AVBF000103 Slopes tripeptide, FDPB VFF neutral (Avbelj, 2000)
|
||||||
|
AVBF000104 Slopes tripeptides, LD VFF neutral (Avbelj, 2000)
|
||||||
|
AVBF000105 Slopes tripeptide, FDPB VFF noside (Avbelj, 2000)
|
||||||
|
AVBF000106 Slopes tripeptide FDPB VFF all (Avbelj, 2000)
|
||||||
|
AVBF000107 Slopes tripeptide FDPB PARSE neutral (Avbelj, 2000)
|
||||||
|
AVBF000108 Slopes dekapeptide, FDPB VFF neutral (Avbelj, 2000)
|
||||||
|
AVBF000109 Slopes proteins, FDPB VFF neutral (Avbelj, 2000)
|
||||||
|
YANJ020101 Side-chain conformation by gaussian evolutionary method (Yang et al., 2002)
|
||||||
|
MITS020101 Amphiphilicity index (Mitaku et al., 2002)
|
||||||
|
TSAJ990101 Volumes including the crystallographic waters using the ProtOr (Tsai et al., 1999)
|
||||||
|
TSAJ990102 Volumes not including the crystallographic waters using the ProtOr (Tsai et al., 1999)
|
||||||
|
COSI940101 Electron-ion interaction potential values (Cosic, 1994)
|
||||||
|
PONP930101 Hydrophobicity scales (Ponnuswamy, 1993)
|
||||||
|
WILM950101 Hydrophobicity coefficient in RP-HPLC, C18 with 0.1%TFA/MeCN/H2O (Wilce et al. 1995)
|
||||||
|
WILM950102 Hydrophobicity coefficient in RP-HPLC, C8 with 0.1%TFA/MeCN/H2O (Wilce et al. 1995)
|
||||||
|
WILM950103 Hydrophobicity coefficient in RP-HPLC, C4 with 0.1%TFA/MeCN/H2O (Wilce et al. 1995)
|
||||||
|
WILM950104 Hydrophobicity coefficient in RP-HPLC, C18 with 0.1%TFA/2-PrOH/MeCN/H2O (Wilce et al. 1995)
|
||||||
|
KUHL950101 Hydrophilicity scale (Kuhn et al., 1995)
|
||||||
|
GUOD860101 Retention coefficient at pH 2 (Guo et al., 1986)
|
||||||
|
JURD980101 Modified Kyte-Doolittle hydrophobicity scale (Juretic et al., 1998)
|
||||||
|
BASU050101 Interactivity scale obtained from the contact matrix (Bastolla et al., 2005)
|
||||||
|
BASU050102 Interactivity scale obtained by maximizing the mean of correlation coefficient over single-domain globular proteins (Bastolla et al., 2005)
|
||||||
|
BASU050103 Interactivity scale obtained by maximizing the mean of correlation coefficient over pairs of sequences sharing the TIM barrel fold (Bastolla et al., 2005)
|
||||||
|
SUYM030101 Linker propensity index (Suyama-Ohara, 2003)
|
||||||
|
PUNT030101 Knowledge-based membrane-propensity scale from 1D_Helix in MPtopo databases (Punta-Maritan, 2003)
|
||||||
|
PUNT030102 Knowledge-based membrane-propensity scale from 3D_Helix in MPtopo databases (Punta-Maritan, 2003)
|
||||||
|
GEOR030101 Linker propensity from all dataset (George-Heringa, 2003)
|
||||||
|
GEOR030102 Linker propensity from 1-linker dataset (George-Heringa, 2003)
|
||||||
|
GEOR030103 Linker propensity from 2-linker dataset (George-Heringa, 2003)
|
||||||
|
GEOR030104 Linker propensity from 3-linker dataset (George-Heringa, 2003)
|
||||||
|
GEOR030105 Linker propensity from small dataset (linker length is less than six residues) (George-Heringa, 2003)
|
||||||
|
GEOR030106 Linker propensity from medium dataset (linker length is between six and 14 residues) (George-Heringa, 2003)
|
||||||
|
GEOR030107 Linker propensity from long dataset (linker length is greater than 14 residues) (George-Heringa, 2003)
|
||||||
|
GEOR030108 Linker propensity from helical (annotated by DSSP) dataset (George-Heringa, 2003)
|
||||||
|
GEOR030109 Linker propensity from non-helical (annotated by DSSP) dataset (George-Heringa, 2003)
|
||||||
|
ZHOH040101 The stability scale from the knowledge-based atom-atom potential (Zhou-Zhou, 2004)
|
||||||
|
ZHOH040102 The relative stability scale extracted from mutation experiments (Zhou-Zhou, 2004)
|
||||||
|
ZHOH040103 Buriability (Zhou-Zhou, 2004)
|
||||||
|
BAEK050101 Linker index (Bae et al., 2005)
|
||||||
|
HARY940101 Mean volumes of residues buried in protein interiors (Harpaz et al., 1994)
|
||||||
|
PONJ960101 Average volumes of residues (Pontius et al., 1996)
|
||||||
|
DIGM050101 Hydrostatic pressure asymmetry index, PAI (Di Giulio, 2005)
|
||||||
|
WOLR790101 Hydrophobicity index (Wolfenden et al., 1979)
|
||||||
|
OLSK800101 Average internal preferences (Olsen, 1980)
|
||||||
|
KIDA850101 Hydrophobicity-related index (Kidera et al., 1985)
|
||||||
|
GUYH850102 Apparent partition energies calculated from Wertz-Scheraga index (Guy, 1985)
|
||||||
|
GUYH850103 Apparent partition energies calculated from Robson-Osguthorpe index (Guy, 1985)
|
||||||
|
GUYH850104 Apparent partition energies calculated from Janin index (Guy, 1985)
|
||||||
|
GUYH850105 Apparent partition energies calculated from Chothia index (Guy, 1985)
|
||||||
|
ROSM880104 Hydropathies of amino acid side chains, neutral form (Roseman, 1988)
|
||||||
|
ROSM880105 Hydropathies of amino acid side chains, pi-values in pH 7.0 (Roseman, 1988)
|
||||||
|
JACR890101 Weights from the IFH scale (Jacobs-White, 1989)
|
||||||
|
COWR900101 Hydrophobicity index, 3.0 pH (Cowan-Whittaker, 1990)
|
||||||
|
BLAS910101 Scaled side chain hydrophobicity values (Black-Mould, 1991)
|
||||||
|
CASG920101 Hydrophobicity scale from native protein structures (Casari-Sippl, 1992)
|
||||||
|
CORJ870101 NNEIG index (Cornette et al., 1987)
|
||||||
|
CORJ870102 SWEIG index (Cornette et al., 1987)
|
||||||
|
CORJ870103 PRIFT index (Cornette et al., 1987)
|
||||||
|
CORJ870104 PRILS index (Cornette et al., 1987)
|
||||||
|
CORJ870105 ALTFT index (Cornette et al., 1987)
|
||||||
|
CORJ870106 ALTLS index (Cornette et al., 1987)
|
||||||
|
CORJ870107 TOTFT index (Cornette et al., 1987)
|
||||||
|
CORJ870108 TOTLS index (Cornette et al., 1987)
|
||||||
|
MIYS990101 Relative partition energies derived by the Bethe approximation (Miyazawa-Jernigan, 1999)
|
||||||
|
MIYS990102 Optimized relative partition energies - method A (Miyazawa-Jernigan, 1999)
|
||||||
|
MIYS990103 Optimized relative partition energies - method B (Miyazawa-Jernigan, 1999)
|
||||||
|
MIYS990104 Optimized relative partition energies - method C (Miyazawa-Jernigan, 1999)
|
||||||
|
MIYS990105 Optimized relative partition energies - method D (Miyazawa-Jernigan, 1999)
|
||||||
|
ENGD860101 Hydrophobicity index (Engelman et al., 1986)
|
||||||
|
FASG890101 Hydrophobicity index (Fasman, 1989)
|
||||||
|
KARS160101 Number of vertices (order of the graph) (Karkbara-Knisley, 2016)
|
||||||
|
KARS160102 Number of edges (size of the graph) (Karkbara-Knisley, 2016)
|
||||||
|
KARS160103 Total weighted degree of the graph (obtained by adding all the weights of all the vertices) (Karkbara-Knisley, 2016)
|
||||||
|
KARS160104 Weighted domination number (Karkbara-Knisley, 2016)
|
||||||
|
KARS160105 Average eccentricity (Karkbara-Knisley, 2016)
|
||||||
|
KARS160106 Radius (minimum eccentricity) (Karkbara-Knisley, 2016)
|
||||||
|
KARS160107 Diameter (maximum eccentricity) (Karkbara-Knisley, 2016)
|
||||||
|
KARS160108 Average weighted degree (total degree, divided by the number of vertices) (Karkbara-Knisley, 2016)
|
||||||
|
KARS160109 Maximum eigenvalue of the weighted Laplacian matrix of the graph (Karkbara-Knisley, 2016)
|
||||||
|
KARS160110 Minimum eigenvalue of the weighted Laplacian matrix of the graph (Karkbara-Knisley, 2016)
|
||||||
|
KARS160111 Average eigenvalue of the Laplacian matrix of the the graph (Karkbara-Knisley, 2016)
|
||||||
|
KARS160112 Second smallest eigenvalue of the Laplacian matrix of the graph (Karkbara-Knisley, 2016)
|
||||||
|
KARS160113 Weighted domination number using the atomic number (Karkbara-Knisley, 2016)
|
||||||
|
KARS160114 Average weighted eccentricity based on the the atomic number (Karkbara-Knisley, 2016)
|
||||||
|
KARS160115 Weighted radius based on the atomic number (minimum eccentricity) (Karkbara-Knisley, 2016)
|
||||||
|
KARS160116 Weighted diameter based on the atomic number (maximum eccentricity) (Karkbara-Knisley, 2016)
|
||||||
|
KARS160117 Total weighted atomic number of the graph (obtained by summing all the atomic number of each of the vertices in the graph) (Karkbara-Knisley, 2016)
|
||||||
|
KARS160118 Average weighted atomic number or degree based on atomic number in the graph (Karkbara-Knisley, 2016)
|
||||||
|
KARS160119 Weighted maximum eigenvalue based on the atomic numbers (Karkbara-Knisley, 2016)
|
||||||
|
KARS160120 Weighted minimum eigenvalue based on the atomic numbers (Karkbara-Knisley, 2016)
|
||||||
|
KARS160121 Weighted average eigenvalue based on the atomic numbers (Karkbara-Knisley, 2016)
|
||||||
|
KARS160122 Weighted second smallest eigenvalue of the weighted Laplacian matrix (Karkbara-Knisley, 2016)
|
||||||
|
List of 94 Amino Acid Matrices in AAindex ver.9.2
|
||||||
|
|
||||||
|
The columns correspond to the AAindex accession number and the description of
|
||||||
|
each matrix.
|
||||||
|
|
||||||
|
ALTS910101 The PAM-120 matrix (Altschul, 1991)
|
||||||
|
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)
|
||||||
|
KOLA920101 Conformational similarity weight matrix (Kolaskar-Kulkarni-Kale, 1992)
|
||||||
|
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)
|
||||||
|
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)
|
||||||
|
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)
|
||||||
|
RISJ880101 Scoring matrix (Risler et al., 1988)
|
||||||
|
TUDE900101 isomorphicity of replacements (Tudos et al., 1990)
|
||||||
|
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)
|
||||||
|
RIER950101 Hydrophobicity scoring matrix (Riek 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)
|
||||||
|
MEHP950101 (Mehta et al., 1995)
|
||||||
|
MEHP950102 (Mehta et al., 1995)
|
||||||
|
MEHP950103 (Mehta et al., 1995)
|
||||||
|
KAPO950101 (Kapp et al., 1995)
|
||||||
|
VOGG950101 (Vogt et al., 1995)
|
||||||
|
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)
|
||||||
|
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)
|
||||||
|
LINK010101 Substitution matrices from an neural network model (Lin et al., 2001)
|
||||||
|
BLAJ010101 Matrix built from structural superposition data for identifying potential remote homologues (Blake-Cohen, 2001)
|
||||||
|
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)
|
||||||
|
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)
|
||||||
|
GIAG010101 Residue substitutions matrix from thermo/mesophilic to psychrophilic enzymes (Gianese et al., 2001)
|
||||||
|
DAYM780302 Log odds matrix for 40 PAMs (Dayhoff et al., 1978)
|
||||||
|
HENS920104 BLOSUM50 substitution matrix (Henikoff-Henikoff, 1992)
|
||||||
|
QUIB020101 STROMA score matrix for the alignment of known distant homologs (Qian-Goldstein, 2002)
|
||||||
|
NAOD960101 Substitution matrix derived from the single residue interchanges at spatially conserved regions of proteins (Naor et al., 1996)
|
||||||
|
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)
|
||||||
|
OGAK980101 Substitution matrix derived from structural alignments by maximizing entropy (Ogata et al., 1998)
|
||||||
|
KANM000101 Substitution matrix (OPTIMA) derived by maximizing discrimination between homologs and non-homologs (Kann et al., 2000)
|
||||||
|
NGPC000101 Substitution matrix (PHAT) built from hydrophobic and transmembrane regions of the Blocks database (Ng et al., 2000)
|
||||||
|
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)
|
||||||
|
CROG050101 Substitution matrix computed from the Dirichlet Mixture Model (Crooks-Brenner, 2005)
|
||||||
|
List of 47 Amino Acid Matrices in AAindex ver.9.2
|
||||||
|
|
||||||
|
The columns correspond to the AAindex accession number and the description of
|
||||||
|
each contact potential matrix.
|
||||||
|
|
||||||
|
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
|
||||||
|
ROBB790102 Interaction energies derived from side chain contacts in the interiors of known protein structures
|
||||||
|
BRYS930101 Distance-dependent statistical potential (only energies of contacts within 0-5 Angstrooms are included)
|
||||||
|
THOP960101 Mixed quasichemical and optimization-based protein contact potential
|
||||||
|
MIRL960101 Statistical potential derived by the maximization of the harmonic mean of Z scores
|
||||||
|
VENM980101 Statistical potential derived by the maximization of the perceptron criterion
|
||||||
|
BASU010101 Optimization-based potential derived by the modified perceptron criterion
|
||||||
|
MIYS850102 Quasichemical energy of transfer of amino acids from water to the protein environment
|
||||||
|
MIYS850103 Quasichemical energy of interactions in an average buried environment
|
||||||
|
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
|
||||||
|
LIWA970101 Modified version of the Miyazawa-Jernigan transfer energy
|
||||||
|
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
|
||||||
|
MOOG990101 Quasichemical potential derived from interfacial regions of protein-protein complexes
|
||||||
|
BETM990101 Modified version of the Miyazawa-Jernigan transfer energy
|
||||||
|
TOBD000101 Optimization-derived potential obtained for small set of decoys
|
||||||
|
TOBD000102 Optimization-derived potential obtained for large set of decoys
|
||||||
|
PARB960101 Statistical contact potential derived by the quasichemical approximation
|
||||||
|
PARB960102 Modified version of the Miyazawa-Jernigan transfer energy
|
||||||
|
KOLA930101 Statistical potential derived by the quasichemical approximation
|
||||||
|
GODA950101 Quasichemical statistical potential derived from buried contacts
|
||||||
|
SKOJ970101 Statistical potential derived by the quasichemical approximation
|
||||||
|
SKOJ000101 Statistical quasichemical potential with the partially composition-corrected pair scale
|
||||||
|
SKOJ000102 Statistical quasichemical potential with the composition-corrected pair scale
|
||||||
|
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
|
||||||
|
MICC010101 Optimization-derived potential
|
||||||
|
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)
|
||||||
|
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)
|
||||||
571
scripts/aa_index_scripts/list_of_indices
Normal file
571
scripts/aa_index_scripts/list_of_indices
Normal file
|
|
@ -0,0 +1,571 @@
|
||||||
|
List of 566 Amino Acid Indices in AAindex ver.9.2
|
||||||
|
|
||||||
|
The columns correspond to the AAindex accession number and the description of
|
||||||
|
each index.
|
||||||
|
|
||||||
|
ANDN920101 alpha-CH chemical shifts (Andersen et al., 1992)
|
||||||
|
ARGP820101 Hydrophobicity index (Argos et al., 1982)
|
||||||
|
ARGP820102 Signal sequence helical potential (Argos et al., 1982)
|
||||||
|
ARGP820103 Membrane-buried preference parameters (Argos et al., 1982)
|
||||||
|
BEGF750101 Conformational parameter of inner helix (Beghin-Dirkx, 1975)
|
||||||
|
BEGF750102 Conformational parameter of beta-structure (Beghin-Dirkx, 1975)
|
||||||
|
BEGF750103 Conformational parameter of beta-turn (Beghin-Dirkx, 1975)
|
||||||
|
BHAR880101 Average flexibility indices (Bhaskaran-Ponnuswamy, 1988)
|
||||||
|
BIGC670101 Residue volume (Bigelow, 1967)
|
||||||
|
BIOV880101 Information value for accessibility; average fraction 35% (Biou et al., 1988)
|
||||||
|
BIOV880102 Information value for accessibility; average fraction 23% (Biou et al., 1988)
|
||||||
|
BROC820101 Retention coefficient in TFA (Browne et al., 1982)
|
||||||
|
BROC820102 Retention coefficient in HFBA (Browne et al., 1982)
|
||||||
|
BULH740101 Transfer free energy to surface (Bull-Breese, 1974)
|
||||||
|
BULH740102 Apparent partial specific volume (Bull-Breese, 1974)
|
||||||
|
BUNA790101 alpha-NH chemical shifts (Bundi-Wuthrich, 1979)
|
||||||
|
BUNA790102 alpha-CH chemical shifts (Bundi-Wuthrich, 1979)
|
||||||
|
BUNA790103 Spin-spin coupling constants 3JHalpha-NH (Bundi-Wuthrich, 1979)
|
||||||
|
BURA740101 Normalized frequency of alpha-helix (Burgess et al., 1974)
|
||||||
|
BURA740102 Normalized frequency of extended structure (Burgess et al., 1974)
|
||||||
|
CHAM810101 Steric parameter (Charton, 1981)
|
||||||
|
CHAM820101 Polarizability parameter (Charton-Charton, 1982)
|
||||||
|
CHAM820102 Free energy of solution in water, kcal/mole (Charton-Charton, 1982)
|
||||||
|
CHAM830101 The Chou-Fasman parameter of the coil conformation (Charton-Charton, 1983)
|
||||||
|
CHAM830102 A parameter defined from the residuals obtained from the best correlation of the Chou-Fasman parameter of beta-sheet (Charton-Charton, 1983)
|
||||||
|
CHAM830103 The number of atoms in the side chain labelled 1+1 (Charton-Charton, 1983)
|
||||||
|
CHAM830104 The number of atoms in the side chain labelled 2+1 (Charton-Charton, 1983)
|
||||||
|
CHAM830105 The number of atoms in the side chain labelled 3+1 (Charton-Charton, 1983)
|
||||||
|
CHAM830106 The number of bonds in the longest chain (Charton-Charton, 1983)
|
||||||
|
CHAM830107 A parameter of charge transfer capability (Charton-Charton, 1983)
|
||||||
|
CHAM830108 A parameter of charge transfer donor capability (Charton-Charton, 1983)
|
||||||
|
CHOC750101 Average volume of buried residue (Chothia, 1975)
|
||||||
|
CHOC760101 Residue accessible surface area in tripeptide (Chothia, 1976)
|
||||||
|
CHOC760102 Residue accessible surface area in folded protein (Chothia, 1976)
|
||||||
|
CHOC760103 Proportion of residues 95% buried (Chothia, 1976)
|
||||||
|
CHOC760104 Proportion of residues 100% buried (Chothia, 1976)
|
||||||
|
CHOP780101 Normalized frequency of beta-turn (Chou-Fasman, 1978a)
|
||||||
|
CHOP780201 Normalized frequency of alpha-helix (Chou-Fasman, 1978b)
|
||||||
|
CHOP780202 Normalized frequency of beta-sheet (Chou-Fasman, 1978b)
|
||||||
|
CHOP780203 Normalized frequency of beta-turn (Chou-Fasman, 1978b)
|
||||||
|
CHOP780204 Normalized frequency of N-terminal helix (Chou-Fasman, 1978b)
|
||||||
|
CHOP780205 Normalized frequency of C-terminal helix (Chou-Fasman, 1978b)
|
||||||
|
CHOP780206 Normalized frequency of N-terminal non helical region (Chou-Fasman, 1978b)
|
||||||
|
CHOP780207 Normalized frequency of C-terminal non helical region (Chou-Fasman, 1978b)
|
||||||
|
CHOP780208 Normalized frequency of N-terminal beta-sheet (Chou-Fasman, 1978b)
|
||||||
|
CHOP780209 Normalized frequency of C-terminal beta-sheet (Chou-Fasman, 1978b)
|
||||||
|
CHOP780210 Normalized frequency of N-terminal non beta region (Chou-Fasman, 1978b)
|
||||||
|
CHOP780211 Normalized frequency of C-terminal non beta region (Chou-Fasman, 1978b)
|
||||||
|
CHOP780212 Frequency of the 1st residue in turn (Chou-Fasman, 1978b)
|
||||||
|
CHOP780213 Frequency of the 2nd residue in turn (Chou-Fasman, 1978b)
|
||||||
|
CHOP780214 Frequency of the 3rd residue in turn (Chou-Fasman, 1978b)
|
||||||
|
CHOP780215 Frequency of the 4th residue in turn (Chou-Fasman, 1978b)
|
||||||
|
CHOP780216 Normalized frequency of the 2nd and 3rd residues in turn (Chou-Fasman, 1978b)
|
||||||
|
CIDH920101 Normalized hydrophobicity scales for alpha-proteins (Cid et al., 1992)
|
||||||
|
CIDH920102 Normalized hydrophobicity scales for beta-proteins (Cid et al., 1992)
|
||||||
|
CIDH920103 Normalized hydrophobicity scales for alpha+beta-proteins (Cid et al., 1992)
|
||||||
|
CIDH920104 Normalized hydrophobicity scales for alpha/beta-proteins (Cid et al., 1992)
|
||||||
|
CIDH920105 Normalized average hydrophobicity scales (Cid et al., 1992)
|
||||||
|
COHE430101 Partial specific volume (Cohn-Edsall, 1943)
|
||||||
|
CRAJ730101 Normalized frequency of middle helix (Crawford et al., 1973)
|
||||||
|
CRAJ730102 Normalized frequency of beta-sheet (Crawford et al., 1973)
|
||||||
|
CRAJ730103 Normalized frequency of turn (Crawford et al., 1973)
|
||||||
|
DAWD720101 Size (Dawson, 1972)
|
||||||
|
DAYM780101 Amino acid composition (Dayhoff et al., 1978a)
|
||||||
|
DAYM780201 Relative mutability (Dayhoff et al., 1978b)
|
||||||
|
DESM900101 Membrane preference for cytochrome b: MPH89 (Degli Esposti et al., 1990)
|
||||||
|
DESM900102 Average membrane preference: AMP07 (Degli Esposti et al., 1990)
|
||||||
|
EISD840101 Consensus normalized hydrophobicity scale (Eisenberg, 1984)
|
||||||
|
EISD860101 Solvation free energy (Eisenberg-McLachlan, 1986)
|
||||||
|
EISD860102 Atom-based hydrophobic moment (Eisenberg-McLachlan, 1986)
|
||||||
|
EISD860103 Direction of hydrophobic moment (Eisenberg-McLachlan, 1986)
|
||||||
|
FASG760101 Molecular weight (Fasman, 1976)
|
||||||
|
FASG760102 Melting point (Fasman, 1976)
|
||||||
|
FASG760103 Optical rotation (Fasman, 1976)
|
||||||
|
FASG760104 pK-N (Fasman, 1976)
|
||||||
|
FASG760105 pK-C (Fasman, 1976)
|
||||||
|
FAUJ830101 Hydrophobic parameter pi (Fauchere-Pliska, 1983)
|
||||||
|
FAUJ880101 Graph shape index (Fauchere et al., 1988)
|
||||||
|
FAUJ880102 Smoothed upsilon steric parameter (Fauchere et al., 1988)
|
||||||
|
FAUJ880103 Normalized van der Waals volume (Fauchere et al., 1988)
|
||||||
|
FAUJ880104 STERIMOL length of the side chain (Fauchere et al., 1988)
|
||||||
|
FAUJ880105 STERIMOL minimum width of the side chain (Fauchere et al., 1988)
|
||||||
|
FAUJ880106 STERIMOL maximum width of the side chain (Fauchere et al., 1988)
|
||||||
|
FAUJ880107 N.m.r. chemical shift of alpha-carbon (Fauchere et al., 1988)
|
||||||
|
FAUJ880108 Localized electrical effect (Fauchere et al., 1988)
|
||||||
|
FAUJ880109 Number of hydrogen bond donors (Fauchere et al., 1988)
|
||||||
|
FAUJ880110 Number of full nonbonding orbitals (Fauchere et al., 1988)
|
||||||
|
FAUJ880111 Positive charge (Fauchere et al., 1988)
|
||||||
|
FAUJ880112 Negative charge (Fauchere et al., 1988)
|
||||||
|
FAUJ880113 pK-a(RCOOH) (Fauchere et al., 1988)
|
||||||
|
FINA770101 Helix-coil equilibrium constant (Finkelstein-Ptitsyn, 1977)
|
||||||
|
FINA910101 Helix initiation parameter at posision i-1 (Finkelstein et al., 1991)
|
||||||
|
FINA910102 Helix initiation parameter at posision i,i+1,i+2 (Finkelstein et al., 1991)
|
||||||
|
FINA910103 Helix termination parameter at posision j-2,j-1,j (Finkelstein et al., 1991)
|
||||||
|
FINA910104 Helix termination parameter at posision j+1 (Finkelstein et al., 1991)
|
||||||
|
GARJ730101 Partition coefficient (Garel et al., 1973)
|
||||||
|
GEIM800101 Alpha-helix indices (Geisow-Roberts, 1980)
|
||||||
|
GEIM800102 Alpha-helix indices for alpha-proteins (Geisow-Roberts, 1980)
|
||||||
|
GEIM800103 Alpha-helix indices for beta-proteins (Geisow-Roberts, 1980)
|
||||||
|
GEIM800104 Alpha-helix indices for alpha/beta-proteins (Geisow-Roberts, 1980)
|
||||||
|
GEIM800105 Beta-strand indices (Geisow-Roberts, 1980)
|
||||||
|
GEIM800106 Beta-strand indices for beta-proteins (Geisow-Roberts, 1980)
|
||||||
|
GEIM800107 Beta-strand indices for alpha/beta-proteins (Geisow-Roberts, 1980)
|
||||||
|
GEIM800108 Aperiodic indices (Geisow-Roberts, 1980)
|
||||||
|
GEIM800109 Aperiodic indices for alpha-proteins (Geisow-Roberts, 1980)
|
||||||
|
GEIM800110 Aperiodic indices for beta-proteins (Geisow-Roberts, 1980)
|
||||||
|
GEIM800111 Aperiodic indices for alpha/beta-proteins (Geisow-Roberts, 1980)
|
||||||
|
GOLD730101 Hydrophobicity factor (Goldsack-Chalifoux, 1973)
|
||||||
|
GOLD730102 Residue volume (Goldsack-Chalifoux, 1973)
|
||||||
|
GRAR740101 Composition (Grantham, 1974)
|
||||||
|
GRAR740102 Polarity (Grantham, 1974)
|
||||||
|
GRAR740103 Volume (Grantham, 1974)
|
||||||
|
GUYH850101 Partition energy (Guy, 1985)
|
||||||
|
HOPA770101 Hydration number (Hopfinger, 1971), Cited by Charton-Charton (1982)
|
||||||
|
HOPT810101 Hydrophilicity value (Hopp-Woods, 1981)
|
||||||
|
HUTJ700101 Heat capacity (Hutchens, 1970)
|
||||||
|
HUTJ700102 Absolute entropy (Hutchens, 1970)
|
||||||
|
HUTJ700103 Entropy of formation (Hutchens, 1970)
|
||||||
|
ISOY800101 Normalized relative frequency of alpha-helix (Isogai et al., 1980)
|
||||||
|
ISOY800102 Normalized relative frequency of extended structure (Isogai et al., 1980)
|
||||||
|
ISOY800103 Normalized relative frequency of bend (Isogai et al., 1980)
|
||||||
|
ISOY800104 Normalized relative frequency of bend R (Isogai et al., 1980)
|
||||||
|
ISOY800105 Normalized relative frequency of bend S (Isogai et al., 1980)
|
||||||
|
ISOY800106 Normalized relative frequency of helix end (Isogai et al., 1980)
|
||||||
|
ISOY800107 Normalized relative frequency of double bend (Isogai et al., 1980)
|
||||||
|
ISOY800108 Normalized relative frequency of coil (Isogai et al., 1980)
|
||||||
|
JANJ780101 Average accessible surface area (Janin et al., 1978)
|
||||||
|
JANJ780102 Percentage of buried residues (Janin et al., 1978)
|
||||||
|
JANJ780103 Percentage of exposed residues (Janin et al., 1978)
|
||||||
|
JANJ790101 Ratio of buried and accessible molar fractions (Janin, 1979)
|
||||||
|
JANJ790102 Transfer free energy (Janin, 1979)
|
||||||
|
JOND750101 Hydrophobicity (Jones, 1975)
|
||||||
|
JOND750102 pK (-COOH) (Jones, 1975)
|
||||||
|
JOND920101 Relative frequency of occurrence (Jones et al., 1992)
|
||||||
|
JOND920102 Relative mutability (Jones et al., 1992)
|
||||||
|
JUKT750101 Amino acid distribution (Jukes et al., 1975)
|
||||||
|
JUNJ780101 Sequence frequency (Jungck, 1978)
|
||||||
|
KANM800101 Average relative probability of helix (Kanehisa-Tsong, 1980)
|
||||||
|
KANM800102 Average relative probability of beta-sheet (Kanehisa-Tsong, 1980)
|
||||||
|
KANM800103 Average relative probability of inner helix (Kanehisa-Tsong, 1980)
|
||||||
|
KANM800104 Average relative probability of inner beta-sheet (Kanehisa-Tsong, 1980)
|
||||||
|
KARP850101 Flexibility parameter for no rigid neighbors (Karplus-Schulz, 1985)
|
||||||
|
KARP850102 Flexibility parameter for one rigid neighbor (Karplus-Schulz, 1985)
|
||||||
|
KARP850103 Flexibility parameter for two rigid neighbors (Karplus-Schulz, 1985)
|
||||||
|
KHAG800101 The Kerr-constant increments (Khanarian-Moore, 1980)
|
||||||
|
KLEP840101 Net charge (Klein et al., 1984)
|
||||||
|
KRIW710101 Side chain interaction parameter (Krigbaum-Rubin, 1971)
|
||||||
|
KRIW790101 Side chain interaction parameter (Krigbaum-Komoriya, 1979)
|
||||||
|
KRIW790102 Fraction of site occupied by water (Krigbaum-Komoriya, 1979)
|
||||||
|
KRIW790103 Side chain volume (Krigbaum-Komoriya, 1979)
|
||||||
|
KYTJ820101 Hydropathy index (Kyte-Doolittle, 1982)
|
||||||
|
LAWE840101 Transfer free energy, CHP/water (Lawson et al., 1984)
|
||||||
|
LEVM760101 Hydrophobic parameter (Levitt, 1976)
|
||||||
|
LEVM760102 Distance between C-alpha and centroid of side chain (Levitt, 1976)
|
||||||
|
LEVM760103 Side chain angle theta(AAR) (Levitt, 1976)
|
||||||
|
LEVM760104 Side chain torsion angle phi(AAAR) (Levitt, 1976)
|
||||||
|
LEVM760105 Radius of gyration of side chain (Levitt, 1976)
|
||||||
|
LEVM760106 van der Waals parameter R0 (Levitt, 1976)
|
||||||
|
LEVM760107 van der Waals parameter epsilon (Levitt, 1976)
|
||||||
|
LEVM780101 Normalized frequency of alpha-helix, with weights (Levitt, 1978)
|
||||||
|
LEVM780102 Normalized frequency of beta-sheet, with weights (Levitt, 1978)
|
||||||
|
LEVM780103 Normalized frequency of reverse turn, with weights (Levitt, 1978)
|
||||||
|
LEVM780104 Normalized frequency of alpha-helix, unweighted (Levitt, 1978)
|
||||||
|
LEVM780105 Normalized frequency of beta-sheet, unweighted (Levitt, 1978)
|
||||||
|
LEVM780106 Normalized frequency of reverse turn, unweighted (Levitt, 1978)
|
||||||
|
LEWP710101 Frequency of occurrence in beta-bends (Lewis et al., 1971)
|
||||||
|
LIFS790101 Conformational preference for all beta-strands (Lifson-Sander, 1979)
|
||||||
|
LIFS790102 Conformational preference for parallel beta-strands (Lifson-Sander, 1979)
|
||||||
|
LIFS790103 Conformational preference for antiparallel beta-strands (Lifson-Sander, 1979)
|
||||||
|
MANP780101 Average surrounding hydrophobicity (Manavalan-Ponnuswamy, 1978)
|
||||||
|
MAXF760101 Normalized frequency of alpha-helix (Maxfield-Scheraga, 1976)
|
||||||
|
MAXF760102 Normalized frequency of extended structure (Maxfield-Scheraga, 1976)
|
||||||
|
MAXF760103 Normalized frequency of zeta R (Maxfield-Scheraga, 1976)
|
||||||
|
MAXF760104 Normalized frequency of left-handed alpha-helix (Maxfield-Scheraga, 1976)
|
||||||
|
MAXF760105 Normalized frequency of zeta L (Maxfield-Scheraga, 1976)
|
||||||
|
MAXF760106 Normalized frequency of alpha region (Maxfield-Scheraga, 1976)
|
||||||
|
MCMT640101 Refractivity (McMeekin et al., 1964), Cited by Jones (1975)
|
||||||
|
MEEJ800101 Retention coefficient in HPLC, pH7.4 (Meek, 1980)
|
||||||
|
MEEJ800102 Retention coefficient in HPLC, pH2.1 (Meek, 1980)
|
||||||
|
MEEJ810101 Retention coefficient in NaClO4 (Meek-Rossetti, 1981)
|
||||||
|
MEEJ810102 Retention coefficient in NaH2PO4 (Meek-Rossetti, 1981)
|
||||||
|
MEIH800101 Average reduced distance for C-alpha (Meirovitch et al., 1980)
|
||||||
|
MEIH800102 Average reduced distance for side chain (Meirovitch et al., 1980)
|
||||||
|
MEIH800103 Average side chain orientation angle (Meirovitch et al., 1980)
|
||||||
|
MIYS850101 Effective partition energy (Miyazawa-Jernigan, 1985)
|
||||||
|
NAGK730101 Normalized frequency of alpha-helix (Nagano, 1973)
|
||||||
|
NAGK730102 Normalized frequency of bata-structure (Nagano, 1973)
|
||||||
|
NAGK730103 Normalized frequency of coil (Nagano, 1973)
|
||||||
|
NAKH900101 AA composition of total proteins (Nakashima et al., 1990)
|
||||||
|
NAKH900102 SD of AA composition of total proteins (Nakashima et al., 1990)
|
||||||
|
NAKH900103 AA composition of mt-proteins (Nakashima et al., 1990)
|
||||||
|
NAKH900104 Normalized composition of mt-proteins (Nakashima et al., 1990)
|
||||||
|
NAKH900105 AA composition of mt-proteins from animal (Nakashima et al., 1990)
|
||||||
|
NAKH900106 Normalized composition from animal (Nakashima et al., 1990)
|
||||||
|
NAKH900107 AA composition of mt-proteins from fungi and plant (Nakashima et al., 1990)
|
||||||
|
NAKH900108 Normalized composition from fungi and plant (Nakashima et al., 1990)
|
||||||
|
NAKH900109 AA composition of membrane proteins (Nakashima et al., 1990)
|
||||||
|
NAKH900110 Normalized composition of membrane proteins (Nakashima et al., 1990)
|
||||||
|
NAKH900111 Transmembrane regions of non-mt-proteins (Nakashima et al., 1990)
|
||||||
|
NAKH900112 Transmembrane regions of mt-proteins (Nakashima et al., 1990)
|
||||||
|
NAKH900113 Ratio of average and computed composition (Nakashima et al., 1990)
|
||||||
|
NAKH920101 AA composition of CYT of single-spanning proteins (Nakashima-Nishikawa, 1992)
|
||||||
|
NAKH920102 AA composition of CYT2 of single-spanning proteins (Nakashima-Nishikawa, 1992)
|
||||||
|
NAKH920103 AA composition of EXT of single-spanning proteins (Nakashima-Nishikawa, 1992)
|
||||||
|
NAKH920104 AA composition of EXT2 of single-spanning proteins (Nakashima-Nishikawa, 1992)
|
||||||
|
NAKH920105 AA composition of MEM of single-spanning proteins (Nakashima-Nishikawa, 1992)
|
||||||
|
NAKH920106 AA composition of CYT of multi-spanning proteins (Nakashima-Nishikawa, 1992)
|
||||||
|
NAKH920107 AA composition of EXT of multi-spanning proteins (Nakashima-Nishikawa, 1992)
|
||||||
|
NAKH920108 AA composition of MEM of multi-spanning proteins (Nakashima-Nishikawa, 1992)
|
||||||
|
NISK800101 8 A contact number (Nishikawa-Ooi, 1980)
|
||||||
|
NISK860101 14 A contact number (Nishikawa-Ooi, 1986)
|
||||||
|
NOZY710101 Transfer energy, organic solvent/water (Nozaki-Tanford, 1971)
|
||||||
|
OOBM770101 Average non-bonded energy per atom (Oobatake-Ooi, 1977)
|
||||||
|
OOBM770102 Short and medium range non-bonded energy per atom (Oobatake-Ooi, 1977)
|
||||||
|
OOBM770103 Long range non-bonded energy per atom (Oobatake-Ooi, 1977)
|
||||||
|
OOBM770104 Average non-bonded energy per residue (Oobatake-Ooi, 1977)
|
||||||
|
OOBM770105 Short and medium range non-bonded energy per residue (Oobatake-Ooi, 1977)
|
||||||
|
OOBM850101 Optimized beta-structure-coil equilibrium constant (Oobatake et al., 1985)
|
||||||
|
OOBM850102 Optimized propensity to form reverse turn (Oobatake et al., 1985)
|
||||||
|
OOBM850103 Optimized transfer energy parameter (Oobatake et al., 1985)
|
||||||
|
OOBM850104 Optimized average non-bonded energy per atom (Oobatake et al., 1985)
|
||||||
|
OOBM850105 Optimized side chain interaction parameter (Oobatake et al., 1985)
|
||||||
|
PALJ810101 Normalized frequency of alpha-helix from LG (Palau et al., 1981)
|
||||||
|
PALJ810102 Normalized frequency of alpha-helix from CF (Palau et al., 1981)
|
||||||
|
PALJ810103 Normalized frequency of beta-sheet from LG (Palau et al., 1981)
|
||||||
|
PALJ810104 Normalized frequency of beta-sheet from CF (Palau et al., 1981)
|
||||||
|
PALJ810105 Normalized frequency of turn from LG (Palau et al., 1981)
|
||||||
|
PALJ810106 Normalized frequency of turn from CF (Palau et al., 1981)
|
||||||
|
PALJ810107 Normalized frequency of alpha-helix in all-alpha class (Palau et al., 1981)
|
||||||
|
PALJ810108 Normalized frequency of alpha-helix in alpha+beta class (Palau et al., 1981)
|
||||||
|
PALJ810109 Normalized frequency of alpha-helix in alpha/beta class (Palau et al., 1981)
|
||||||
|
PALJ810110 Normalized frequency of beta-sheet in all-beta class (Palau et al., 1981)
|
||||||
|
PALJ810111 Normalized frequency of beta-sheet in alpha+beta class (Palau et al., 1981)
|
||||||
|
PALJ810112 Normalized frequency of beta-sheet in alpha/beta class (Palau et al., 1981)
|
||||||
|
PALJ810113 Normalized frequency of turn in all-alpha class (Palau et al., 1981)
|
||||||
|
PALJ810114 Normalized frequency of turn in all-beta class (Palau et al., 1981)
|
||||||
|
PALJ810115 Normalized frequency of turn in alpha+beta class (Palau et al., 1981)
|
||||||
|
PALJ810116 Normalized frequency of turn in alpha/beta class (Palau et al., 1981)
|
||||||
|
PARJ860101 HPLC parameter (Parker et al., 1986)
|
||||||
|
PLIV810101 Partition coefficient (Pliska et al., 1981)
|
||||||
|
PONP800101 Surrounding hydrophobicity in folded form (Ponnuswamy et al., 1980)
|
||||||
|
PONP800102 Average gain in surrounding hydrophobicity (Ponnuswamy et al., 1980)
|
||||||
|
PONP800103 Average gain ratio in surrounding hydrophobicity (Ponnuswamy et al., 1980)
|
||||||
|
PONP800104 Surrounding hydrophobicity in alpha-helix (Ponnuswamy et al., 1980)
|
||||||
|
PONP800105 Surrounding hydrophobicity in beta-sheet (Ponnuswamy et al., 1980)
|
||||||
|
PONP800106 Surrounding hydrophobicity in turn (Ponnuswamy et al., 1980)
|
||||||
|
PONP800107 Accessibility reduction ratio (Ponnuswamy et al., 1980)
|
||||||
|
PONP800108 Average number of surrounding residues (Ponnuswamy et al., 1980)
|
||||||
|
PRAM820101 Intercept in regression analysis (Prabhakaran-Ponnuswamy, 1982)
|
||||||
|
PRAM820102 Slope in regression analysis x 1.0E1 (Prabhakaran-Ponnuswamy, 1982)
|
||||||
|
PRAM820103 Correlation coefficient in regression analysis (Prabhakaran-Ponnuswamy, 1982)
|
||||||
|
PRAM900101 Hydrophobicity (Prabhakaran, 1990)
|
||||||
|
PRAM900102 Relative frequency in alpha-helix (Prabhakaran, 1990)
|
||||||
|
PRAM900103 Relative frequency in beta-sheet (Prabhakaran, 1990)
|
||||||
|
PRAM900104 Relative frequency in reverse-turn (Prabhakaran, 1990)
|
||||||
|
PTIO830101 Helix-coil equilibrium constant (Ptitsyn-Finkelstein, 1983)
|
||||||
|
PTIO830102 Beta-coil equilibrium constant (Ptitsyn-Finkelstein, 1983)
|
||||||
|
QIAN880101 Weights for alpha-helix at the window position of -6 (Qian-Sejnowski, 1988)
|
||||||
|
QIAN880102 Weights for alpha-helix at the window position of -5 (Qian-Sejnowski, 1988)
|
||||||
|
QIAN880103 Weights for alpha-helix at the window position of -4 (Qian-Sejnowski, 1988)
|
||||||
|
QIAN880104 Weights for alpha-helix at the window position of -3 (Qian-Sejnowski, 1988)
|
||||||
|
QIAN880105 Weights for alpha-helix at the window position of -2 (Qian-Sejnowski, 1988)
|
||||||
|
QIAN880106 Weights for alpha-helix at the window position of -1 (Qian-Sejnowski, 1988)
|
||||||
|
QIAN880107 Weights for alpha-helix at the window position of 0 (Qian-Sejnowski, 1988)
|
||||||
|
QIAN880108 Weights for alpha-helix at the window position of 1 (Qian-Sejnowski, 1988)
|
||||||
|
QIAN880109 Weights for alpha-helix at the window position of 2 (Qian-Sejnowski, 1988)
|
||||||
|
QIAN880110 Weights for alpha-helix at the window position of 3 (Qian-Sejnowski, 1988)
|
||||||
|
QIAN880111 Weights for alpha-helix at the window position of 4 (Qian-Sejnowski, 1988)
|
||||||
|
QIAN880112 Weights for alpha-helix at the window position of 5 (Qian-Sejnowski, 1988)
|
||||||
|
QIAN880113 Weights for alpha-helix at the window position of 6 (Qian-Sejnowski, 1988)
|
||||||
|
QIAN880114 Weights for beta-sheet at the window position of -6 (Qian-Sejnowski, 1988)
|
||||||
|
QIAN880115 Weights for beta-sheet at the window position of -5 (Qian-Sejnowski, 1988)
|
||||||
|
QIAN880116 Weights for beta-sheet at the window position of -4 (Qian-Sejnowski, 1988)
|
||||||
|
QIAN880117 Weights for beta-sheet at the window position of -3 (Qian-Sejnowski, 1988)
|
||||||
|
QIAN880118 Weights for beta-sheet at the window position of -2 (Qian-Sejnowski, 1988)
|
||||||
|
QIAN880119 Weights for beta-sheet at the window position of -1 (Qian-Sejnowski, 1988)
|
||||||
|
QIAN880120 Weights for beta-sheet at the window position of 0 (Qian-Sejnowski, 1988)
|
||||||
|
QIAN880121 Weights for beta-sheet at the window position of 1 (Qian-Sejnowski, 1988)
|
||||||
|
QIAN880122 Weights for beta-sheet at the window position of 2 (Qian-Sejnowski, 1988)
|
||||||
|
QIAN880123 Weights for beta-sheet at the window position of 3 (Qian-Sejnowski, 1988)
|
||||||
|
QIAN880124 Weights for beta-sheet at the window position of 4 (Qian-Sejnowski, 1988)
|
||||||
|
QIAN880125 Weights for beta-sheet at the window position of 5 (Qian-Sejnowski, 1988)
|
||||||
|
QIAN880126 Weights for beta-sheet at the window position of 6 (Qian-Sejnowski, 1988)
|
||||||
|
QIAN880127 Weights for coil at the window position of -6 (Qian-Sejnowski, 1988)
|
||||||
|
QIAN880128 Weights for coil at the window position of -5 (Qian-Sejnowski, 1988)
|
||||||
|
QIAN880129 Weights for coil at the window position of -4 (Qian-Sejnowski, 1988)
|
||||||
|
QIAN880130 Weights for coil at the window position of -3 (Qian-Sejnowski, 1988)
|
||||||
|
QIAN880131 Weights for coil at the window position of -2 (Qian-Sejnowski, 1988)
|
||||||
|
QIAN880132 Weights for coil at the window position of -1 (Qian-Sejnowski, 1988)
|
||||||
|
QIAN880133 Weights for coil at the window position of 0 (Qian-Sejnowski, 1988)
|
||||||
|
QIAN880134 Weights for coil at the window position of 1 (Qian-Sejnowski, 1988)
|
||||||
|
QIAN880135 Weights for coil at the window position of 2 (Qian-Sejnowski, 1988)
|
||||||
|
QIAN880136 Weights for coil at the window position of 3 (Qian-Sejnowski, 1988)
|
||||||
|
QIAN880137 Weights for coil at the window position of 4 (Qian-Sejnowski, 1988)
|
||||||
|
QIAN880138 Weights for coil at the window position of 5 (Qian-Sejnowski, 1988)
|
||||||
|
QIAN880139 Weights for coil at the window position of 6 (Qian-Sejnowski, 1988)
|
||||||
|
RACS770101 Average reduced distance for C-alpha (Rackovsky-Scheraga, 1977)
|
||||||
|
RACS770102 Average reduced distance for side chain (Rackovsky-Scheraga, 1977)
|
||||||
|
RACS770103 Side chain orientational preference (Rackovsky-Scheraga, 1977)
|
||||||
|
RACS820101 Average relative fractional occurrence in A0(i) (Rackovsky-Scheraga, 1982)
|
||||||
|
RACS820102 Average relative fractional occurrence in AR(i) (Rackovsky-Scheraga, 1982)
|
||||||
|
RACS820103 Average relative fractional occurrence in AL(i) (Rackovsky-Scheraga, 1982)
|
||||||
|
RACS820104 Average relative fractional occurrence in EL(i) (Rackovsky-Scheraga, 1982)
|
||||||
|
RACS820105 Average relative fractional occurrence in E0(i) (Rackovsky-Scheraga, 1982)
|
||||||
|
RACS820106 Average relative fractional occurrence in ER(i) (Rackovsky-Scheraga, 1982)
|
||||||
|
RACS820107 Average relative fractional occurrence in A0(i-1) (Rackovsky-Scheraga, 1982)
|
||||||
|
RACS820108 Average relative fractional occurrence in AR(i-1) (Rackovsky-Scheraga, 1982)
|
||||||
|
RACS820109 Average relative fractional occurrence in AL(i-1) (Rackovsky-Scheraga, 1982)
|
||||||
|
RACS820110 Average relative fractional occurrence in EL(i-1) (Rackovsky-Scheraga, 1982)
|
||||||
|
RACS820111 Average relative fractional occurrence in E0(i-1) (Rackovsky-Scheraga, 1982)
|
||||||
|
RACS820112 Average relative fractional occurrence in ER(i-1) (Rackovsky-Scheraga, 1982)
|
||||||
|
RACS820113 Value of theta(i) (Rackovsky-Scheraga, 1982)
|
||||||
|
RACS820114 Value of theta(i-1) (Rackovsky-Scheraga, 1982)
|
||||||
|
RADA880101 Transfer free energy from chx to wat (Radzicka-Wolfenden, 1988)
|
||||||
|
RADA880102 Transfer free energy from oct to wat (Radzicka-Wolfenden, 1988)
|
||||||
|
RADA880103 Transfer free energy from vap to chx (Radzicka-Wolfenden, 1988)
|
||||||
|
RADA880104 Transfer free energy from chx to oct (Radzicka-Wolfenden, 1988)
|
||||||
|
RADA880105 Transfer free energy from vap to oct (Radzicka-Wolfenden, 1988)
|
||||||
|
RADA880106 Accessible surface area (Radzicka-Wolfenden, 1988)
|
||||||
|
RADA880107 Energy transfer from out to in(95%buried) (Radzicka-Wolfenden, 1988)
|
||||||
|
RADA880108 Mean polarity (Radzicka-Wolfenden, 1988)
|
||||||
|
RICJ880101 Relative preference value at N" (Richardson-Richardson, 1988)
|
||||||
|
RICJ880102 Relative preference value at N' (Richardson-Richardson, 1988)
|
||||||
|
RICJ880103 Relative preference value at N-cap (Richardson-Richardson, 1988)
|
||||||
|
RICJ880104 Relative preference value at N1 (Richardson-Richardson, 1988)
|
||||||
|
RICJ880105 Relative preference value at N2 (Richardson-Richardson, 1988)
|
||||||
|
RICJ880106 Relative preference value at N3 (Richardson-Richardson, 1988)
|
||||||
|
RICJ880107 Relative preference value at N4 (Richardson-Richardson, 1988)
|
||||||
|
RICJ880108 Relative preference value at N5 (Richardson-Richardson, 1988)
|
||||||
|
RICJ880109 Relative preference value at Mid (Richardson-Richardson, 1988)
|
||||||
|
RICJ880110 Relative preference value at C5 (Richardson-Richardson, 1988)
|
||||||
|
RICJ880111 Relative preference value at C4 (Richardson-Richardson, 1988)
|
||||||
|
RICJ880112 Relative preference value at C3 (Richardson-Richardson, 1988)
|
||||||
|
RICJ880113 Relative preference value at C2 (Richardson-Richardson, 1988)
|
||||||
|
RICJ880114 Relative preference value at C1 (Richardson-Richardson, 1988)
|
||||||
|
RICJ880115 Relative preference value at C-cap (Richardson-Richardson, 1988)
|
||||||
|
RICJ880116 Relative preference value at C' (Richardson-Richardson, 1988)
|
||||||
|
RICJ880117 Relative preference value at C" (Richardson-Richardson, 1988)
|
||||||
|
ROBB760101 Information measure for alpha-helix (Robson-Suzuki, 1976)
|
||||||
|
ROBB760102 Information measure for N-terminal helix (Robson-Suzuki, 1976)
|
||||||
|
ROBB760103 Information measure for middle helix (Robson-Suzuki, 1976)
|
||||||
|
ROBB760104 Information measure for C-terminal helix (Robson-Suzuki, 1976)
|
||||||
|
ROBB760105 Information measure for extended (Robson-Suzuki, 1976)
|
||||||
|
ROBB760106 Information measure for pleated-sheet (Robson-Suzuki, 1976)
|
||||||
|
ROBB760107 Information measure for extended without H-bond (Robson-Suzuki, 1976)
|
||||||
|
ROBB760108 Information measure for turn (Robson-Suzuki, 1976)
|
||||||
|
ROBB760109 Information measure for N-terminal turn (Robson-Suzuki, 1976)
|
||||||
|
ROBB760110 Information measure for middle turn (Robson-Suzuki, 1976)
|
||||||
|
ROBB760111 Information measure for C-terminal turn (Robson-Suzuki, 1976)
|
||||||
|
ROBB760112 Information measure for coil (Robson-Suzuki, 1976)
|
||||||
|
ROBB760113 Information measure for loop (Robson-Suzuki, 1976)
|
||||||
|
ROBB790101 Hydration free energy (Robson-Osguthorpe, 1979)
|
||||||
|
ROSG850101 Mean area buried on transfer (Rose et al., 1985)
|
||||||
|
ROSG850102 Mean fractional area loss (Rose et al., 1985)
|
||||||
|
ROSM880101 Side chain hydropathy, uncorrected for solvation (Roseman, 1988)
|
||||||
|
ROSM880102 Side chain hydropathy, corrected for solvation (Roseman, 1988)
|
||||||
|
ROSM880103 Loss of Side chain hydropathy by helix formation (Roseman, 1988)
|
||||||
|
SIMZ760101 Transfer free energy (Simon, 1976), Cited by Charton-Charton (1982)
|
||||||
|
SNEP660101 Principal component I (Sneath, 1966)
|
||||||
|
SNEP660102 Principal component II (Sneath, 1966)
|
||||||
|
SNEP660103 Principal component III (Sneath, 1966)
|
||||||
|
SNEP660104 Principal component IV (Sneath, 1966)
|
||||||
|
SUEM840101 Zimm-Bragg parameter s at 20 C (Sueki et al., 1984)
|
||||||
|
SUEM840102 Zimm-Bragg parameter sigma x 1.0E4 (Sueki et al., 1984)
|
||||||
|
SWER830101 Optimal matching hydrophobicity (Sweet-Eisenberg, 1983)
|
||||||
|
TANS770101 Normalized frequency of alpha-helix (Tanaka-Scheraga, 1977)
|
||||||
|
TANS770102 Normalized frequency of isolated helix (Tanaka-Scheraga, 1977)
|
||||||
|
TANS770103 Normalized frequency of extended structure (Tanaka-Scheraga, 1977)
|
||||||
|
TANS770104 Normalized frequency of chain reversal R (Tanaka-Scheraga, 1977)
|
||||||
|
TANS770105 Normalized frequency of chain reversal S (Tanaka-Scheraga, 1977)
|
||||||
|
TANS770106 Normalized frequency of chain reversal D (Tanaka-Scheraga, 1977)
|
||||||
|
TANS770107 Normalized frequency of left-handed helix (Tanaka-Scheraga, 1977)
|
||||||
|
TANS770108 Normalized frequency of zeta R (Tanaka-Scheraga, 1977)
|
||||||
|
TANS770109 Normalized frequency of coil (Tanaka-Scheraga, 1977)
|
||||||
|
TANS770110 Normalized frequency of chain reversal (Tanaka-Scheraga, 1977)
|
||||||
|
VASM830101 Relative population of conformational state A (Vasquez et al., 1983)
|
||||||
|
VASM830102 Relative population of conformational state C (Vasquez et al., 1983)
|
||||||
|
VASM830103 Relative population of conformational state E (Vasquez et al., 1983)
|
||||||
|
VELV850101 Electron-ion interaction potential (Veljkovic et al., 1985)
|
||||||
|
VENT840101 Bitterness (Venanzi, 1984)
|
||||||
|
VHEG790101 Transfer free energy to lipophilic phase (von Heijne-Blomberg, 1979)
|
||||||
|
WARP780101 Average interactions per side chain atom (Warme-Morgan, 1978)
|
||||||
|
WEBA780101 RF value in high salt chromatography (Weber-Lacey, 1978)
|
||||||
|
WERD780101 Propensity to be buried inside (Wertz-Scheraga, 1978)
|
||||||
|
WERD780102 Free energy change of epsilon(i) to epsilon(ex) (Wertz-Scheraga, 1978)
|
||||||
|
WERD780103 Free energy change of alpha(Ri) to alpha(Rh) (Wertz-Scheraga, 1978)
|
||||||
|
WERD780104 Free energy change of epsilon(i) to alpha(Rh) (Wertz-Scheraga, 1978)
|
||||||
|
WOEC730101 Polar requirement (Woese, 1973)
|
||||||
|
WOLR810101 Hydration potential (Wolfenden et al., 1981)
|
||||||
|
WOLS870101 Principal property value z1 (Wold et al., 1987)
|
||||||
|
WOLS870102 Principal property value z2 (Wold et al., 1987)
|
||||||
|
WOLS870103 Principal property value z3 (Wold et al., 1987)
|
||||||
|
YUTK870101 Unfolding Gibbs energy in water, pH7.0 (Yutani et al., 1987)
|
||||||
|
YUTK870102 Unfolding Gibbs energy in water, pH9.0 (Yutani et al., 1987)
|
||||||
|
YUTK870103 Activation Gibbs energy of unfolding, pH7.0 (Yutani et al., 1987)
|
||||||
|
YUTK870104 Activation Gibbs energy of unfolding, pH9.0 (Yutani et al., 1987)
|
||||||
|
ZASB820101 Dependence of partition coefficient on ionic strength (Zaslavsky et al., 1982)
|
||||||
|
ZIMJ680101 Hydrophobicity (Zimmerman et al., 1968)
|
||||||
|
ZIMJ680102 Bulkiness (Zimmerman et al., 1968)
|
||||||
|
ZIMJ680103 Polarity (Zimmerman et al., 1968)
|
||||||
|
ZIMJ680104 Isoelectric point (Zimmerman et al., 1968)
|
||||||
|
ZIMJ680105 RF rank (Zimmerman et al., 1968)
|
||||||
|
AURR980101 Normalized positional residue frequency at helix termini N4'(Aurora-Rose, 1998)
|
||||||
|
AURR980102 Normalized positional residue frequency at helix termini N"' (Aurora-Rose, 1998)
|
||||||
|
AURR980103 Normalized positional residue frequency at helix termini N" (Aurora-Rose, 1998)
|
||||||
|
AURR980104 Normalized positional residue frequency at helix termini N'(Aurora-Rose, 1998)
|
||||||
|
AURR980105 Normalized positional residue frequency at helix termini Nc (Aurora-Rose, 1998)
|
||||||
|
AURR980106 Normalized positional residue frequency at helix termini N1 (Aurora-Rose, 1998)
|
||||||
|
AURR980107 Normalized positional residue frequency at helix termini N2 (Aurora-Rose, 1998)
|
||||||
|
AURR980108 Normalized positional residue frequency at helix termini N3 (Aurora-Rose, 1998)
|
||||||
|
AURR980109 Normalized positional residue frequency at helix termini N4 (Aurora-Rose, 1998)
|
||||||
|
AURR980110 Normalized positional residue frequency at helix termini N5 (Aurora-Rose, 1998)
|
||||||
|
AURR980111 Normalized positional residue frequency at helix termini C5 (Aurora-Rose, 1998)
|
||||||
|
AURR980112 Normalized positional residue frequency at helix termini C4 (Aurora-Rose, 1998)
|
||||||
|
AURR980113 Normalized positional residue frequency at helix termini C3 (Aurora-Rose, 1998)
|
||||||
|
AURR980114 Normalized positional residue frequency at helix termini C2 (Aurora-Rose, 1998)
|
||||||
|
AURR980115 Normalized positional residue frequency at helix termini C1 (Aurora-Rose, 1998)
|
||||||
|
AURR980116 Normalized positional residue frequency at helix termini Cc (Aurora-Rose, 1998)
|
||||||
|
AURR980117 Normalized positional residue frequency at helix termini C' (Aurora-Rose, 1998)
|
||||||
|
AURR980118 Normalized positional residue frequency at helix termini C" (Aurora-Rose, 1998)
|
||||||
|
AURR980119 Normalized positional residue frequency at helix termini C"' (Aurora-Rose, 1998)
|
||||||
|
AURR980120 Normalized positional residue frequency at helix termini C4' (Aurora-Rose, 1998)
|
||||||
|
ONEK900101 Delta G values for the peptides extrapolated to 0 M urea (O'Neil-DeGrado, 1990)
|
||||||
|
ONEK900102 Helix formation parameters (delta delta G) (O'Neil-DeGrado, 1990)
|
||||||
|
VINM940101 Normalized flexibility parameters (B-values), average (Vihinen et al., 1994)
|
||||||
|
VINM940102 Normalized flexibility parameters (B-values) for each residue surrounded by none rigid neighbours (Vihinen et al., 1994)
|
||||||
|
VINM940103 Normalized flexibility parameters (B-values) for each residue surrounded by one rigid neighbours (Vihinen et al., 1994)
|
||||||
|
VINM940104 Normalized flexibility parameters (B-values) for each residue surrounded by two rigid neighbours (Vihinen et al., 1994)
|
||||||
|
MUNV940101 Free energy in alpha-helical conformation (Munoz-Serrano, 1994)
|
||||||
|
MUNV940102 Free energy in alpha-helical region (Munoz-Serrano, 1994)
|
||||||
|
MUNV940103 Free energy in beta-strand conformation (Munoz-Serrano, 1994)
|
||||||
|
MUNV940104 Free energy in beta-strand region (Munoz-Serrano, 1994)
|
||||||
|
MUNV940105 Free energy in beta-strand region (Munoz-Serrano, 1994)
|
||||||
|
WIMW960101 Free energies of transfer of AcWl-X-LL peptides from bilayer interface to water (Wimley-White, 1996)
|
||||||
|
KIMC930101 Thermodynamic beta sheet propensity (Kim-Berg, 1993)
|
||||||
|
MONM990101 Turn propensity scale for transmembrane helices (Monne et al., 1999)
|
||||||
|
BLAM930101 Alpha helix propensity of position 44 in T4 lysozyme (Blaber et al., 1993)
|
||||||
|
PARS000101 p-Values of mesophilic proteins based on the distributions of B values (Parthasarathy-Murthy, 2000)
|
||||||
|
PARS000102 p-Values of thermophilic proteins based on the distributions of B values (Parthasarathy-Murthy, 2000)
|
||||||
|
KUMS000101 Distribution of amino acid residues in the 18 non-redundant families of thermophilic proteins (Kumar et al., 2000)
|
||||||
|
KUMS000102 Distribution of amino acid residues in the 18 non-redundant families of mesophilic proteins (Kumar et al., 2000)
|
||||||
|
KUMS000103 Distribution of amino acid residues in the alpha-helices in thermophilic proteins (Kumar et al., 2000)
|
||||||
|
KUMS000104 Distribution of amino acid residues in the alpha-helices in mesophilic proteins (Kumar et al., 2000)
|
||||||
|
TAKK010101 Side-chain contribution to protein stability (kJ/mol) (Takano-Yutani, 2001)
|
||||||
|
FODM020101 Propensity of amino acids within pi-helices (Fodje-Al-Karadaghi, 2002)
|
||||||
|
NADH010101 Hydropathy scale based on self-information values in the two-state model (5% accessibility) (Naderi-Manesh et al., 2001)
|
||||||
|
NADH010102 Hydropathy scale based on self-information values in the two-state model (9% accessibility) (Naderi-Manesh et al., 2001)
|
||||||
|
NADH010103 Hydropathy scale based on self-information values in the two-state model (16% accessibility) (Naderi-Manesh et al., 2001)
|
||||||
|
NADH010104 Hydropathy scale based on self-information values in the two-state model (20% accessibility) (Naderi-Manesh et al., 2001)
|
||||||
|
NADH010105 Hydropathy scale based on self-information values in the two-state model (25% accessibility) (Naderi-Manesh et al., 2001)
|
||||||
|
NADH010106 Hydropathy scale based on self-information values in the two-state model (36% accessibility) (Naderi-Manesh et al., 2001)
|
||||||
|
NADH010107 Hydropathy scale based on self-information values in the two-state model (50% accessibility) (Naderi-Manesh et al., 2001)
|
||||||
|
MONM990201 Averaged turn propensities in a transmembrane helix (Monne et al., 1999)
|
||||||
|
KOEP990101 Alpha-helix propensity derived from designed sequences (Koehl-Levitt, 1999)
|
||||||
|
KOEP990102 Beta-sheet propensity derived from designed sequences (Koehl-Levitt, 1999)
|
||||||
|
CEDJ970101 Composition of amino acids in extracellular proteins (percent) (Cedano et al., 1997)
|
||||||
|
CEDJ970102 Composition of amino acids in anchored proteins (percent) (Cedano et al., 1997)
|
||||||
|
CEDJ970103 Composition of amino acids in membrane proteins (percent) (Cedano et al., 1997)
|
||||||
|
CEDJ970104 Composition of amino acids in intracellular proteins (percent) (Cedano et al., 1997)
|
||||||
|
CEDJ970105 Composition of amino acids in nuclear proteins (percent) (Cedano et al., 1997)
|
||||||
|
FUKS010101 Surface composition of amino acids in intracellular proteins of thermophiles (percent) (Fukuchi-Nishikawa, 2001)
|
||||||
|
FUKS010102 Surface composition of amino acids in intracellular proteins of mesophiles (percent) (Fukuchi-Nishikawa, 2001)
|
||||||
|
FUKS010103 Surface composition of amino acids in extracellular proteins of mesophiles (percent) (Fukuchi-Nishikawa, 2001)
|
||||||
|
FUKS010104 Surface composition of amino acids in nuclear proteins (percent) (Fukuchi-Nishikawa, 2001)
|
||||||
|
FUKS010105 Interior composition of amino acids in intracellular proteins of thermophiles (percent) (Fukuchi-Nishikawa, 2001)
|
||||||
|
FUKS010106 Interior composition of amino acids in intracellular proteins of mesophiles (percent) (Fukuchi-Nishikawa, 2001)
|
||||||
|
FUKS010107 Interior composition of amino acids in extracellular proteins of mesophiles (percent) (Fukuchi-Nishikawa, 2001)
|
||||||
|
FUKS010108 Interior composition of amino acids in nuclear proteins (percent) (Fukuchi-Nishikawa, 2001)
|
||||||
|
FUKS010109 Entire chain composition of amino acids in intracellular proteins of thermophiles (percent) (Fukuchi-Nishikawa, 2001)
|
||||||
|
FUKS010110 Entire chain composition of amino acids in intracellular proteins of mesophiles (percent) (Fukuchi-Nishikawa, 2001)
|
||||||
|
FUKS010111 Entire chain composition of amino acids in extracellular proteins of mesophiles (percent) (Fukuchi-Nishikawa, 2001)
|
||||||
|
FUKS010112 Entire chain compositino of amino acids in nuclear proteins (percent) (Fukuchi-Nishikawa, 2001)
|
||||||
|
AVBF000101 Screening coefficients gamma, local (Avbelj, 2000)
|
||||||
|
AVBF000102 Screening coefficients gamma, non-local (Avbelj, 2000)
|
||||||
|
AVBF000103 Slopes tripeptide, FDPB VFF neutral (Avbelj, 2000)
|
||||||
|
AVBF000104 Slopes tripeptides, LD VFF neutral (Avbelj, 2000)
|
||||||
|
AVBF000105 Slopes tripeptide, FDPB VFF noside (Avbelj, 2000)
|
||||||
|
AVBF000106 Slopes tripeptide FDPB VFF all (Avbelj, 2000)
|
||||||
|
AVBF000107 Slopes tripeptide FDPB PARSE neutral (Avbelj, 2000)
|
||||||
|
AVBF000108 Slopes dekapeptide, FDPB VFF neutral (Avbelj, 2000)
|
||||||
|
AVBF000109 Slopes proteins, FDPB VFF neutral (Avbelj, 2000)
|
||||||
|
YANJ020101 Side-chain conformation by gaussian evolutionary method (Yang et al., 2002)
|
||||||
|
MITS020101 Amphiphilicity index (Mitaku et al., 2002)
|
||||||
|
TSAJ990101 Volumes including the crystallographic waters using the ProtOr (Tsai et al., 1999)
|
||||||
|
TSAJ990102 Volumes not including the crystallographic waters using the ProtOr (Tsai et al., 1999)
|
||||||
|
COSI940101 Electron-ion interaction potential values (Cosic, 1994)
|
||||||
|
PONP930101 Hydrophobicity scales (Ponnuswamy, 1993)
|
||||||
|
WILM950101 Hydrophobicity coefficient in RP-HPLC, C18 with 0.1%TFA/MeCN/H2O (Wilce et al. 1995)
|
||||||
|
WILM950102 Hydrophobicity coefficient in RP-HPLC, C8 with 0.1%TFA/MeCN/H2O (Wilce et al. 1995)
|
||||||
|
WILM950103 Hydrophobicity coefficient in RP-HPLC, C4 with 0.1%TFA/MeCN/H2O (Wilce et al. 1995)
|
||||||
|
WILM950104 Hydrophobicity coefficient in RP-HPLC, C18 with 0.1%TFA/2-PrOH/MeCN/H2O (Wilce et al. 1995)
|
||||||
|
KUHL950101 Hydrophilicity scale (Kuhn et al., 1995)
|
||||||
|
GUOD860101 Retention coefficient at pH 2 (Guo et al., 1986)
|
||||||
|
JURD980101 Modified Kyte-Doolittle hydrophobicity scale (Juretic et al., 1998)
|
||||||
|
BASU050101 Interactivity scale obtained from the contact matrix (Bastolla et al., 2005)
|
||||||
|
BASU050102 Interactivity scale obtained by maximizing the mean of correlation coefficient over single-domain globular proteins (Bastolla et al., 2005)
|
||||||
|
BASU050103 Interactivity scale obtained by maximizing the mean of correlation coefficient over pairs of sequences sharing the TIM barrel fold (Bastolla et al., 2005)
|
||||||
|
SUYM030101 Linker propensity index (Suyama-Ohara, 2003)
|
||||||
|
PUNT030101 Knowledge-based membrane-propensity scale from 1D_Helix in MPtopo databases (Punta-Maritan, 2003)
|
||||||
|
PUNT030102 Knowledge-based membrane-propensity scale from 3D_Helix in MPtopo databases (Punta-Maritan, 2003)
|
||||||
|
GEOR030101 Linker propensity from all dataset (George-Heringa, 2003)
|
||||||
|
GEOR030102 Linker propensity from 1-linker dataset (George-Heringa, 2003)
|
||||||
|
GEOR030103 Linker propensity from 2-linker dataset (George-Heringa, 2003)
|
||||||
|
GEOR030104 Linker propensity from 3-linker dataset (George-Heringa, 2003)
|
||||||
|
GEOR030105 Linker propensity from small dataset (linker length is less than six residues) (George-Heringa, 2003)
|
||||||
|
GEOR030106 Linker propensity from medium dataset (linker length is between six and 14 residues) (George-Heringa, 2003)
|
||||||
|
GEOR030107 Linker propensity from long dataset (linker length is greater than 14 residues) (George-Heringa, 2003)
|
||||||
|
GEOR030108 Linker propensity from helical (annotated by DSSP) dataset (George-Heringa, 2003)
|
||||||
|
GEOR030109 Linker propensity from non-helical (annotated by DSSP) dataset (George-Heringa, 2003)
|
||||||
|
ZHOH040101 The stability scale from the knowledge-based atom-atom potential (Zhou-Zhou, 2004)
|
||||||
|
ZHOH040102 The relative stability scale extracted from mutation experiments (Zhou-Zhou, 2004)
|
||||||
|
ZHOH040103 Buriability (Zhou-Zhou, 2004)
|
||||||
|
BAEK050101 Linker index (Bae et al., 2005)
|
||||||
|
HARY940101 Mean volumes of residues buried in protein interiors (Harpaz et al., 1994)
|
||||||
|
PONJ960101 Average volumes of residues (Pontius et al., 1996)
|
||||||
|
DIGM050101 Hydrostatic pressure asymmetry index, PAI (Di Giulio, 2005)
|
||||||
|
WOLR790101 Hydrophobicity index (Wolfenden et al., 1979)
|
||||||
|
OLSK800101 Average internal preferences (Olsen, 1980)
|
||||||
|
KIDA850101 Hydrophobicity-related index (Kidera et al., 1985)
|
||||||
|
GUYH850102 Apparent partition energies calculated from Wertz-Scheraga index (Guy, 1985)
|
||||||
|
GUYH850103 Apparent partition energies calculated from Robson-Osguthorpe index (Guy, 1985)
|
||||||
|
GUYH850104 Apparent partition energies calculated from Janin index (Guy, 1985)
|
||||||
|
GUYH850105 Apparent partition energies calculated from Chothia index (Guy, 1985)
|
||||||
|
ROSM880104 Hydropathies of amino acid side chains, neutral form (Roseman, 1988)
|
||||||
|
ROSM880105 Hydropathies of amino acid side chains, pi-values in pH 7.0 (Roseman, 1988)
|
||||||
|
JACR890101 Weights from the IFH scale (Jacobs-White, 1989)
|
||||||
|
COWR900101 Hydrophobicity index, 3.0 pH (Cowan-Whittaker, 1990)
|
||||||
|
BLAS910101 Scaled side chain hydrophobicity values (Black-Mould, 1991)
|
||||||
|
CASG920101 Hydrophobicity scale from native protein structures (Casari-Sippl, 1992)
|
||||||
|
CORJ870101 NNEIG index (Cornette et al., 1987)
|
||||||
|
CORJ870102 SWEIG index (Cornette et al., 1987)
|
||||||
|
CORJ870103 PRIFT index (Cornette et al., 1987)
|
||||||
|
CORJ870104 PRILS index (Cornette et al., 1987)
|
||||||
|
CORJ870105 ALTFT index (Cornette et al., 1987)
|
||||||
|
CORJ870106 ALTLS index (Cornette et al., 1987)
|
||||||
|
CORJ870107 TOTFT index (Cornette et al., 1987)
|
||||||
|
CORJ870108 TOTLS index (Cornette et al., 1987)
|
||||||
|
MIYS990101 Relative partition energies derived by the Bethe approximation (Miyazawa-Jernigan, 1999)
|
||||||
|
MIYS990102 Optimized relative partition energies - method A (Miyazawa-Jernigan, 1999)
|
||||||
|
MIYS990103 Optimized relative partition energies - method B (Miyazawa-Jernigan, 1999)
|
||||||
|
MIYS990104 Optimized relative partition energies - method C (Miyazawa-Jernigan, 1999)
|
||||||
|
MIYS990105 Optimized relative partition energies - method D (Miyazawa-Jernigan, 1999)
|
||||||
|
ENGD860101 Hydrophobicity index (Engelman et al., 1986)
|
||||||
|
FASG890101 Hydrophobicity index (Fasman, 1989)
|
||||||
|
KARS160101 Number of vertices (order of the graph) (Karkbara-Knisley, 2016)
|
||||||
|
KARS160102 Number of edges (size of the graph) (Karkbara-Knisley, 2016)
|
||||||
|
KARS160103 Total weighted degree of the graph (obtained by adding all the weights of all the vertices) (Karkbara-Knisley, 2016)
|
||||||
|
KARS160104 Weighted domination number (Karkbara-Knisley, 2016)
|
||||||
|
KARS160105 Average eccentricity (Karkbara-Knisley, 2016)
|
||||||
|
KARS160106 Radius (minimum eccentricity) (Karkbara-Knisley, 2016)
|
||||||
|
KARS160107 Diameter (maximum eccentricity) (Karkbara-Knisley, 2016)
|
||||||
|
KARS160108 Average weighted degree (total degree, divided by the number of vertices) (Karkbara-Knisley, 2016)
|
||||||
|
KARS160109 Maximum eigenvalue of the weighted Laplacian matrix of the graph (Karkbara-Knisley, 2016)
|
||||||
|
KARS160110 Minimum eigenvalue of the weighted Laplacian matrix of the graph (Karkbara-Knisley, 2016)
|
||||||
|
KARS160111 Average eigenvalue of the Laplacian matrix of the the graph (Karkbara-Knisley, 2016)
|
||||||
|
KARS160112 Second smallest eigenvalue of the Laplacian matrix of the graph (Karkbara-Knisley, 2016)
|
||||||
|
KARS160113 Weighted domination number using the atomic number (Karkbara-Knisley, 2016)
|
||||||
|
KARS160114 Average weighted eccentricity based on the the atomic number (Karkbara-Knisley, 2016)
|
||||||
|
KARS160115 Weighted radius based on the atomic number (minimum eccentricity) (Karkbara-Knisley, 2016)
|
||||||
|
KARS160116 Weighted diameter based on the atomic number (maximum eccentricity) (Karkbara-Knisley, 2016)
|
||||||
|
KARS160117 Total weighted atomic number of the graph (obtained by summing all the atomic number of each of the vertices in the graph) (Karkbara-Knisley, 2016)
|
||||||
|
KARS160118 Average weighted atomic number or degree based on atomic number in the graph (Karkbara-Knisley, 2016)
|
||||||
|
KARS160119 Weighted maximum eigenvalue based on the atomic numbers (Karkbara-Knisley, 2016)
|
||||||
|
KARS160120 Weighted minimum eigenvalue based on the atomic numbers (Karkbara-Knisley, 2016)
|
||||||
|
KARS160121 Weighted average eigenvalue based on the atomic numbers (Karkbara-Knisley, 2016)
|
||||||
|
KARS160122 Weighted second smallest eigenvalue of the weighted Laplacian matrix (Karkbara-Knisley, 2016)
|
||||||
99
scripts/aa_index_scripts/list_of_matrices
Normal file
99
scripts/aa_index_scripts/list_of_matrices
Normal file
|
|
@ -0,0 +1,99 @@
|
||||||
|
List of 94 Amino Acid Matrices in AAindex ver.9.2
|
||||||
|
|
||||||
|
The columns correspond to the AAindex accession number and the description of
|
||||||
|
each matrix.
|
||||||
|
|
||||||
|
ALTS910101 The PAM-120 matrix (Altschul, 1991)
|
||||||
|
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)
|
||||||
|
KOLA920101 Conformational similarity weight matrix (Kolaskar-Kulkarni-Kale, 1992)
|
||||||
|
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)
|
||||||
|
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)
|
||||||
|
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)
|
||||||
|
RISJ880101 Scoring matrix (Risler et al., 1988)
|
||||||
|
TUDE900101 isomorphicity of replacements (Tudos et al., 1990)
|
||||||
|
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)
|
||||||
|
RIER950101 Hydrophobicity scoring matrix (Riek 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)
|
||||||
|
MEHP950101 (Mehta et al., 1995)
|
||||||
|
MEHP950102 (Mehta et al., 1995)
|
||||||
|
MEHP950103 (Mehta et al., 1995)
|
||||||
|
KAPO950101 (Kapp et al., 1995)
|
||||||
|
VOGG950101 (Vogt et al., 1995)
|
||||||
|
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)
|
||||||
|
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)
|
||||||
|
LINK010101 Substitution matrices from an neural network model (Lin et al., 2001)
|
||||||
|
BLAJ010101 Matrix built from structural superposition data for identifying potential remote homologues (Blake-Cohen, 2001)
|
||||||
|
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)
|
||||||
|
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)
|
||||||
|
GIAG010101 Residue substitutions matrix from thermo/mesophilic to psychrophilic enzymes (Gianese et al., 2001)
|
||||||
|
DAYM780302 Log odds matrix for 40 PAMs (Dayhoff et al., 1978)
|
||||||
|
HENS920104 BLOSUM50 substitution matrix (Henikoff-Henikoff, 1992)
|
||||||
|
QUIB020101 STROMA score matrix for the alignment of known distant homologs (Qian-Goldstein, 2002)
|
||||||
|
NAOD960101 Substitution matrix derived from the single residue interchanges at spatially conserved regions of proteins (Naor et al., 1996)
|
||||||
|
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)
|
||||||
|
OGAK980101 Substitution matrix derived from structural alignments by maximizing entropy (Ogata et al., 1998)
|
||||||
|
KANM000101 Substitution matrix (OPTIMA) derived by maximizing discrimination between homologs and non-homologs (Kann et al., 2000)
|
||||||
|
NGPC000101 Substitution matrix (PHAT) built from hydrophobic and transmembrane regions of the Blocks database (Ng et al., 2000)
|
||||||
|
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)
|
||||||
|
CROG050101 Substitution matrix computed from the Dirichlet Mixture Model (Crooks-Brenner, 2005)
|
||||||
52
scripts/aa_index_scripts/list_of_potentials
Normal file
52
scripts/aa_index_scripts/list_of_potentials
Normal file
|
|
@ -0,0 +1,52 @@
|
||||||
|
List of 47 Amino Acid Matrices in AAindex ver.9.2
|
||||||
|
|
||||||
|
The columns correspond to the AAindex accession number and the description of
|
||||||
|
each contact potential matrix.
|
||||||
|
|
||||||
|
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
|
||||||
|
ROBB790102 Interaction energies derived from side chain contacts in the interiors of known protein structures
|
||||||
|
BRYS930101 Distance-dependent statistical potential (only energies of contacts within 0-5 Angstrooms are included)
|
||||||
|
THOP960101 Mixed quasichemical and optimization-based protein contact potential
|
||||||
|
MIRL960101 Statistical potential derived by the maximization of the harmonic mean of Z scores
|
||||||
|
VENM980101 Statistical potential derived by the maximization of the perceptron criterion
|
||||||
|
BASU010101 Optimization-based potential derived by the modified perceptron criterion
|
||||||
|
MIYS850102 Quasichemical energy of transfer of amino acids from water to the protein environment
|
||||||
|
MIYS850103 Quasichemical energy of interactions in an average buried environment
|
||||||
|
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
|
||||||
|
LIWA970101 Modified version of the Miyazawa-Jernigan transfer energy
|
||||||
|
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
|
||||||
|
MOOG990101 Quasichemical potential derived from interfacial regions of protein-protein complexes
|
||||||
|
BETM990101 Modified version of the Miyazawa-Jernigan transfer energy
|
||||||
|
TOBD000101 Optimization-derived potential obtained for small set of decoys
|
||||||
|
TOBD000102 Optimization-derived potential obtained for large set of decoys
|
||||||
|
PARB960101 Statistical contact potential derived by the quasichemical approximation
|
||||||
|
PARB960102 Modified version of the Miyazawa-Jernigan transfer energy
|
||||||
|
KOLA930101 Statistical potential derived by the quasichemical approximation
|
||||||
|
GODA950101 Quasichemical statistical potential derived from buried contacts
|
||||||
|
SKOJ970101 Statistical potential derived by the quasichemical approximation
|
||||||
|
SKOJ000101 Statistical quasichemical potential with the partially composition-corrected pair scale
|
||||||
|
SKOJ000102 Statistical quasichemical potential with the composition-corrected pair scale
|
||||||
|
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
|
||||||
|
MICC010101 Optimization-derived potential
|
||||||
|
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)
|
||||||
|
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)
|
||||||
|
|
@ -1,27 +0,0 @@
|
||||||
#!/bin/sh
|
|
||||||
drug=${1:-pyrazinamide}
|
|
||||||
gene=${2:-pnca}
|
|
||||||
|
|
||||||
aa_python="/home/tanu/git/LSHTM_analysis/scripts/aa_index_scripts/aaindex/get_scores.py"
|
|
||||||
snp_dir="/home/tanu/git/Data/${drug}"
|
|
||||||
aa_outfile="/home/tanu/git/Data/${drug}/output/aa_index/${gene}_aa"
|
|
||||||
|
|
||||||
echo "Running for drug: ${drug} and gene ${gene}. Output to: ${aa_outfile}"
|
|
||||||
for i in $(cat ${snp_dir}/output/${gene}_mcsm_formatted_snps.csv)
|
|
||||||
do
|
|
||||||
echo -n "${i}," >> $aa_outfile
|
|
||||||
python $aa_python $snp_dir/input/${gene}_complex.pdb A $i >> $aa_outfile
|
|
||||||
done
|
|
||||||
# How I want it to run
|
|
||||||
#gene = "pncA" # force it to be lowercase
|
|
||||||
#chain = "A"
|
|
||||||
#mutfile = "/home/tanu/git/Data/output/<gene>_mcsm_snps.csv"
|
|
||||||
#mut = for i in mutfile
|
|
||||||
|
|
||||||
|
|
||||||
#$1 = "/home/tanu/git/Data/input/<gene>_complex.pdb
|
|
||||||
#$2 = chain
|
|
||||||
#$3 = mut
|
|
||||||
|
|
||||||
#python /home/tanu/git/LSHTM_analysis/scripts/aa_index_scripts/aaindex/get_scores.py $1 $2 $3
|
|
||||||
|
|
||||||
|
|
@ -1,9 +1,11 @@
|
||||||
#!/bin/sh
|
#!/bin/sh
|
||||||
#python /home/sportelli/Desktop/Important_Code/structural/aaindex/get_scores.py /home/sportelli/Desktop/Project_2_rpoB/leprae/RMLE_B_RFP.pdb C P28A
|
#python /home/sportelli/Desktop/Important_Code/structural/aaindex/get_scores.py /home/sportelli/Desktop/Project_2_rpoB/leprae/RMLE_B_RFP.pdb C P28A
|
||||||
#python /home/tanu/git/LSHTM_analysis/scripts/aa_index_scripts/aaindex/get_scores.py /home/tanu/git/LSHTM_analysis/scripts/aa_index_scripts/pnca_complex.pdb A L4S
|
#python /home/tanu/git/LSHTM_analysis/scripts/aa_index_scripts/aaindex/get_scores.py /home/tanu/git/LSHTM_analysis/scripts/aa_index_scripts/pnca_complex.pdb A L4S
|
||||||
#python /home/tanu/git/LSHTM_analysis/scripts/aa_index_scripts/aaindex/get_scores.py /home/tanu/git/Data/pyrazinamide/input/pnca_complex.pdb A L4S
|
python /home/tanu/git/LSHTM_analysis/scripts/aa_index_scripts/aaindex/get_scores.py /home/tanu/git/Data/pyrazinamide/input/pnca_complex.pdb A L4S
|
||||||
for i in $(cat /home/tanu/git/Data/pyrazinamide/output/*mcsm_snps*); do echo -n "${i}," >>/home/tanu/git/Data/pyrazinamide/output/aa_index/pnca_aa; python /home/tanu/git/LSHTM_analysis/scripts/aa_index_scripts/aaindex/get_scores.py /home/tanu/git/Data/pyrazinamide/input/pnca_complex.pdb A $i >> /home/tanu/git/Data/pyrazinamide/output/aa_index/pnca_aa; done
|
|
||||||
|
#----------------------
|
||||||
# How I want it to run
|
# How I want it to run
|
||||||
|
#---------------------
|
||||||
#drug = "pyrazinamide"
|
#drug = "pyrazinamide"
|
||||||
#gene = "pncA" # force it to be lowercase
|
#gene = "pncA" # force it to be lowercase
|
||||||
#chain = "A"
|
#chain = "A"
|
||||||
|
|
@ -17,3 +19,4 @@ for i in $(cat /home/tanu/git/Data/pyrazinamide/output/*mcsm_snps*); do echo -n
|
||||||
|
|
||||||
#python /home/tanu/git/LSHTM_analysis/scripts/aa_index_scripts/aaindex/get_scores.py $1 $2 $3
|
#python /home/tanu/git/LSHTM_analysis/scripts/aa_index_scripts/aaindex/get_scores.py $1 $2 $3
|
||||||
|
|
||||||
|
#for i in $(cat /home/tanu/git/Data/pyrazinamide/output/*mcsm_snps*); do echo -n "${i}," >>/home/tanu/git/Data/pyrazinamide/output/aa_index/pnca_aa; python /home/tanu/git/LSHTM_analysis/scripts/aa_index_scripts/aaindex/get_scores.py /home/tanu/git/Data/pyrazinamide/input/pnca_complex.pdb A $i >> /home/tanu/git/Data/pyrazinamide/output/aa_index/pnca_aa; done
|
||||||
31
scripts/aa_index_scripts/run_aaindex.sh
Executable file
31
scripts/aa_index_scripts/run_aaindex.sh
Executable file
|
|
@ -0,0 +1,31 @@
|
||||||
|
#!/bin/sh
|
||||||
|
drug=${1:-pyrazinamide}
|
||||||
|
gene=${2:-pnca}
|
||||||
|
chain=${3:-A}
|
||||||
|
|
||||||
|
aa_python="/home/tanu/git/LSHTM_analysis/scripts/aa_index_scripts/aaindex/get_scores.py"
|
||||||
|
snp_dir="/home/tanu/git/Data/${drug}"
|
||||||
|
aa_outfile="/home/tanu/git/Data/${drug}/output/aa_index/${gene}_aa.csv"
|
||||||
|
|
||||||
|
echo "Running for drug: ${drug} and gene ${gene}
|
||||||
|
Input from: ${snp_dir}/input/${gene}_complex.pdb
|
||||||
|
Chain: ${chain}
|
||||||
|
Output to: ${aa_outfile}"
|
||||||
|
|
||||||
|
cat ADD_aa_header.csv > $aa_outfile
|
||||||
|
|
||||||
|
for i in $(cat ${snp_dir}/output/${gene}_mcsm_formatted_snps.csv)
|
||||||
|
do
|
||||||
|
echo -n "${i}," >> $aa_outfile
|
||||||
|
python $aa_python $snp_dir/input/${gene}_complex.pdb $chain $i >> $aa_outfile
|
||||||
|
done
|
||||||
|
|
||||||
|
|
||||||
|
# TO RUN
|
||||||
|
# gene should be in lowercase
|
||||||
|
# ~/git/LSHTM_analysis/scripts/aa_index_scripts/run_aaindex.sh cycloserine alr A
|
||||||
|
# ~/git/LSHTM_analysis/scripts/aa_index_scripts/run_aaindex.sh ethambutol embb B
|
||||||
|
# ~/git/LSHTM_analysis/scripts/aa_index_scripts/run_aaindex.sh streptomycin gid A
|
||||||
|
# ~/git/LSHTM_analysis/scripts/aa_index_scripts/run_aaindex.sh isoniazid katg A
|
||||||
|
# ~/git/LSHTM_analysis/scripts/aa_index_scripts/run_aaindex.sh pyrazinamide pnca A
|
||||||
|
# ~/git/LSHTM_analysis/scripts/aa_index_scripts/run_aaindex.sh rifampicin rpob A
|
||||||
Loading…
Add table
Add a link
Reference in a new issue