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)
