The PAM-120 matrix (Altschul, 1991) 
 Amino acid substitution matrices from an information theoretic perspective
 J. Mol. Biol. 219, 555-565 (1991)
  0.723486
 Log-odds scoring matrix collected in 6.4-8.7 PAM (Benner et al., 1994) 
 Benner, S.A., Cohen, M.A. and Gonnet, G.H.
 Amino acid substitution during functionally constrained divergent
 evolution of protein sequences
 Protein Engineering 7, 1323-1332 (1994)
  0.710595
 Log-odds scoring matrix collected in 22-29 PAM (Benner et al., 1994) 
 Benner, S.A., Cohen, M.A. and Gonnet, G.H.
 Amino acid substitution during functionally constrained divergent
 evolution of protein sequences
 Protein Engineering 7, 1323-1332 (1994)
  0.717775
 Log-odds scoring matrix collected in 74-100 PAM (Benner et al., 1994) 
 Amino acid substitution during functionally constrained divergent
 evolution of protein sequences
 Protein Engineering 7, 1323-1332 (1994)
  0.719109
 Genetic code matrix (Benner et al., 1994)
 Benner, S.A., Cohen, M.A. and Gonnet, G.H.
 Amino acid substitution during functionally constrained divergent
 evolution of protein sequences
 Protein Engineering 7, 1323-1332 (1994) 
  0.686660
 Residue replace ability matrix (Cserzo et al., 1994) 
 Cserzo, M., Bernassau, J.-M., Simon, I. and Maigret, B.
 New alignment strategy for transmembrane proteins
 J. Mol. Biol. 243, 388-396 (1994)
  0.714221
 Log odds matrix for 250 PAMs (Dayhoff et al., 1978) 
 Dayhoff, M.O., Schwartz, R.M. and Orcutt, B.C.
 A model of evolutionary change in proteins
 In "Atlas of Protein Sequence and Structure", Vol.5, Suppl.3 (Dayhoff,
 M.O., ed.), National Biomedical Research Foundation, Washington, D.C.,
 p.352 (1978)
  0.700737
 Structure-Genetic matrix (Feng et al., 1985) 
 Feng, D.F., Johnson, M.S. and Doolittle, R.F.
 Aligning amino acid sequences: comparison of commonly used methods
 J. Mol. Evol. 21, 112-125 (1985)
  0.703750
 Mutation values for the interconversion of amino acid pairs (Fitch, 1966) 
 Fitch, W.M.
 An improved method of testing for evolutionary homology
 J. Mol. Biol. 16, 9-16 (1966)
  -0.617526
 Hydrophobicity scoring matrix (George et al., 1990) 
 George, D.G., Barker, W.C. and Hunt, L.T.
 Mutation data matrix and its uses
 Methods Enzymol. 183, 333-351 (1990)
  0.386996
 The mutation matrix for initially aligning (Gonnet et al., 1992) 
 Gonnet, G.H., Cohen, M.A. and Benner, S.A.
 Exhaustive matching of the entire protein sequence database
 Science 256, 1443-1445 (1992)
  0.715068
 Chemical distance (Grantham, 1974) 
 Grantham, R.
 Amino acid difference formula to help explain protein evolution
 Science 185, 862-864 (1974)
  -0.556011
 BLOSUM45 substitution matrix (Henikoff-Henikoff, 1992) 
 Henikoff, S. and Henikoff, J.G.
 Amino acid substitution matrices from protein blocks
 Proc. Natl. Acad. Sci. USA 89, 10915-10919 (1992)
  0.808715
 BLOSUM62 substitution matrix (Henikoff-Henikoff, 1992) 
 Henikoff, S. and Henikoff, J.G.
 Amino acid substitution matrices from protein blocks
 Proc. Natl. Acad. Sci. USA 89, 10915-10919 (1992)
  0.801578
 BLOSUM80 substitution matrix (Henikoff-Henikoff, 1992) 
 Henikoff, S. and Henikoff, J.G.
 Amino acid substitution matrices from protein blocks
 Proc. Natl. Acad. Sci. USA 89, 10915-10919 (1992)
  0.800058
 Structure-based amino acid scoring table (Johnson-Overington, 1993) 
 Johnson, M.S. and Overington, J.P.
 A structural basis for sequence comparisons
 An evaluation of scoring methodologies
 J. Mol. Biol. 233, 716-738 (1993)
  0.795346
 The 250 PAM PET91 matrix (Jones et al., 1992) 
 ones, D.T., Taylor, W.R. and Thornton, J.M.
 The rapid generation of mutation data matrices from protein sequences
 CABIOS 8, 275-282 (1992)
  0.734110
 The 250 PAM transmembrane protein exchange matrix (Jones et al., 1994) 
 Jones, D.T., Taylor, W.R. and Thornton, J.M.
 A mutation data matrix for transmembrane proteins
 FEBS Lett. 339, 269-275 (1994)
  0.611155
 Conformational similarity weight matrix (Kolaskar-Kulkarni-Kale, 1992) 
 Kolaskar, A.S. and Kulkarni-Kale, U.
 Sequence alignment approach to pick up conformationally similar
 protein fragments
 J. Mol. Biol. 223, 1053-1061 (1992)
  0.500443
 The secondary structure similarity matrix (Levin et al., 1986)
 Levin, J.M., Robson, B. and Garnier, J.
 An algorithm for secondary structure determination in proteins based on
 sequence similarity
 FEBS Lett. 205, 303-308 (1986) 
  0.669530
 Structure-based comparison table for outside other class (Luthy et al., 1991) 
 Luthy, R., McLachlan, A.D. and Eisenberg, D.
 Secondary structure-based profiles: Use of structure-conserving scoring
 tables in searching protein sequence databases for structural similarities
 Proteins 10, 229-239 (1991)
  0.733690
 Structure-based comparison table for inside other class (Luthy et al., 1991) 
 Luthy, R., McLachlan, A.D. and Eisenberg, D.
 Secondary structure-based profiles: Use of structure-conserving scoring
 tables in searching protein sequence databases for structural similarities
 Proteins 10, 229-239 (1991)
  0.590333
 Structure-based comparison table for outside alpha class (Luthy et al., 1991) 
 Luthy, R., McLachlan, A.D. and Eisenberg, D.
 Secondary structure-based profiles: Use of structure-conserving scoring
 tables in searching protein sequence databases for structural similarities
 Proteins 10, 229-239 (1991)
  0.622272
 Structure-based comparison table for inside alpha class (Luthy et al., 1991) 
 Luthy, R., McLachlan, A.D. and Eisenberg, D.
 Secondary structure-based profiles: Use of structure-conserving scoring
 tables in searching protein sequence databases for structural similarities
 Proteins 10, 229-239 (1991)
  0.511780
 Structure-based comparison table for outside beta class (Luthy et al., 1991) 
 Luthy, R., McLachlan, A.D. and Eisenberg, D.
 Secondary structure-based profiles: Use of structure-conserving scoring
 tables in searching protein sequence databases for structural similarities
 Proteins 10, 229-239 (1991)
  0.716834
 Structure-based comparison table for inside beta class (Luthy et al., 1991) 
 Luthy, R., McLachlan, A.D. and Eisenberg, D.
 Secondary structure-based profiles: Use of structure-conserving scoring
 tables in searching protein sequence databases for structural similarities
 Proteins 10, 229-239 (1991)
  0.589351
 Structure-based comparison table for other class (Luthy et al., 1991) 
 Luthy, R., McLachlan, A.D. and Eisenberg, D.
 Secondary structure-based profiles: Use of structure-conserving scoring
 tables in searching protein sequence databases for structural similarities
 Proteins 10, 229-239 (1991)
  0.722409
 Structure-based comparison table for alpha helix class (Luthy et al., 1991) 
 Luthy, R., McLachlan, A.D. and Eisenberg, D.
 Secondary structure-based profiles: Use of structure-conserving scoring
 tables in searching protein sequence databases for structural similarities
 Proteins 10, 229-239 (1991)
  0.613977
 Structure-based comparison table for beta strand class (Luthy et al., 1991) 
 Luthy, R., McLachlan, A.D. and Eisenberg, D.
 Secondary structure-based profiles: Use of structure-conserving scoring
 tables in searching protein sequence databases for structural similarities
 Proteins 10, 229-239 (1991)
  0.705973
 The similarity of pairs of amino acids (McLachlan, 1971) 
 McLachlan, A.D.
 Tests for comparing related amino-acid sequences
 cytochrome c and cytochrome c551
 J. Mol. Biol. 61, 409-424 (1971)
  0.784998
 Chemical similarity scores (McLachlan, 1972) 
 McLachlan, A.D.
 Repeating sequences and gene duplication in proteins
 J. Mol. Biol. 64, 417-437 (1972)
  0.819956
 Base-substitution-protein-stability matrix (Miyazawa-Jernigan, 1993) 
 Miyazawa, S. and Jernigan, R.L.
 A new substitution matrix for protein sequence searches based on
 contact frequencies in protein structures
 Protein Engineering 6, 267-278 (1993)
  0.562128
 Amino acid pair distance (Miyata et al., 1979) 
 Miyata, T., Miyazawa, S. and Yasunaga, T.
 Two types of amino acid substitutions in protein evolution
 J. Mol. Evol. 12, 219-236 (1979)
  -0.540405
 EMPAR matrix (Mohana Rao, 1987) 
 Mohana Rao, J.K.
 New scoring matrix for amino acid residue exchanges based on residue
 characteristic physical parameters
 Int. J. Peptide Protein Res. 29, 276-281 (1987)
  0.616446
 Structure-derived correlation matrix 1 (Niefind-Schomburg, 1991) 
 Niefind, K. and Schomburg, D.
 Amino acid similarity coefficients for protein modeling and sequence
 alignment derived from main-chain folding angles
 J. Mol. Biol. 219, 481-497 (1991)
  0.665370
 Structure-derived correlation matrix 2 (Niefind-Schomburg, 1991) 
 Niefind, K. and Schomburg, D.
 Amino acid similarity coefficients for protein modeling and sequence
 alignment derived from main-chain folding angles
 J. Mol. Biol. 219, 481-497 (1991)
  0.648426
 STR matrix from structure-based alignments (Overington et al., 1992) 
 Overington, J., Donnelly, D., Johnson, M.S., Sali, A. and Blundell, T.L.
 Environment-specific amino acid substitution tables: tertiary templates
 and prediction of protein folds
 Prot. Sci. 1, 216-226 (1992)
  0.782376
 Cross-correlation coefficients of preference factors 
 main chain (Qu et al., 1993)
 Qu, C., Lai, L., Xu, X. and Tang, Y.
 Phyletic relationships of protein structures based on spatial prefernce
 of residues
 J. Mol. Evol. 36, 67-78 (1993)
  0.509058
 Cross-correlation coefficients of preference factors side chain (Qu et al., 1993)
 Qu, C., Lai, L., Xu, X. and Tang, Y.
 Phyletic relationships of protein structures based on spatial prefernce
 of residues
 J. Mol. Evol. 36, 67-78 (1993)
  0.446368
 The mutant distance based on spatial preference factor (Qu et al., 1993) 
 Qu, C., Lai, L., Xu, X. and Tang, Y.
 Phyletic relationships of protein structures based on spatial prefernce
 of residues
 J. Mol. Evol. 36, 67-78 (1993)
  0.611150
 Scoring matrix (Risler et al., 1988) 
 Risler, J.L., Delorme, M.O., Delacroix, H. and Henaut, A.
 Amino acid substitutions in structurally related proteins
 A pattern recognition approach
 Determination of a new and efficient scoring matrix
 J. Mol. Biol. 204, 1019-1029 (1988)
  0.437658
 isomorphicity of replacements (Tudos et al., 1990) 
 Tudos, E., Cserzo, M. and Simon, I.
 Predicting isomorphic residue replacements for protein design
 Int. J. Peptide Protein Res. 36, 236-239 (1990)
  0.781205
 The single residue substitution matrix from interchanges of spatially 
 neighbouring residues (Azarya-Sprinzak et al., 1997) 
 Azarya-Sprinzak, E., Naor, D., Wolfson, H.J. and Nussinov, R.
 Interchanges of spatially neighbouring residues in structurally conserved
 environments.
 Protein Engineering 10, 1109-1122 (1997)
  0.307445
 The substitution matrix derived from spatially conserved motifs 
   (Azarya-Sprinzak et al., 1997)
 Azarya-Sprinzak, E., Naor, D., Wolfson, H.J. and Nussinov, R.
 Interchanges of spatially neighbouring residues in structurally conserved
 environments.
 Protein Engineering 10, 1109-1122 (1997)
  0.290511
 Hydrophobicity scoring matrix (Riek et al., 1995) 
 Riek, R.P., Handschumacher, M.D., Sung, S.S., Tan, M., Glynias, M.J.,
 Schluchter, M.D., Novotny, J. and Graham, R.M.
 Evolutionary conservation of both the hydrophilic and hydrophobic nature of
 transmembrane residues.
 J. Theor. Biol. 172, 245-258 (1995)
  0.174474
 WAC matrix constructed from amino acid comparative profiles (Wei et al., 1997) 
 Wei, L., Altman, R.B. and Chang, J.T.
 Using the radial distributions of physical features to compare amino
 acid environments and align amino acid sequences.
 Pac. Symp. Biocomput. 1997 5, 465-476 (1997)
  0.490456
 Difference matrix obtained by subtracting the BLOSUM62 from the WAC 
 matrix (Wei et al., 1997)
 Wei, L., Altman, R.B. and Chang, J.T.
 Using the radial distributions of physical features to compare amino
 acid environments and align amino acid sequences.
 Pac. Symp. Biocomput. 1997 5, 465-476 (1997)
  -0.299557