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H ALTS910101
D The PAM-120 matrix (Altschul, 1991)
R PMID:2051488
A Altschul, S.F.
T Amino acid substitution matrices from an information theoretic perspective
J J. Mol. Biol. 219, 555-565 (1991)
M rows = ARNDCQEGHILKMFPSTWYV, cols = ARNDCQEGHILKMFPSTWYV
      3.
     -3.      6.
      0.     -1.      4.
      0.     -3.      2.      5.
     -3.     -4.     -5.     -7.      9.
     -1.      1.      0.      1.     -7.      6.
      0.     -3.      1.      3.     -7.      2.      5.
      1.     -4.      0.      0.     -5.     -3.     -1.      5.
     -3.      1.      2.      0.     -4.      3.     -1.     -4.      7.
     -1.     -2.     -2.     -3.     -3.     -3.     -3.     -4.     -4.      6.
     -3.     -4.     -4.     -5.     -7.     -2.     -4.     -5.     -3.      1.      5.
     -2.      2.      1.     -1.     -7.      0.     -1.     -3.     -2.     -2.     -4.      5.
     -2.     -1.     -3.     -4.     -6.     -1.     -4.     -4.     -4.      1.      3.      0.      8.
     -4.     -4.     -4.     -7.     -6.     -6.     -6.     -5.     -2.      0.      0.     -6.     -1.      8.
      1.     -1.     -2.     -2.     -3.      0.     -1.     -2.     -1.     -3.     -3.     -2.     -3.     -5.      6.
      1.     -1.      1.      0.     -1.     -2.     -1.      1.     -2.     -2.     -4.     -1.     -2.     -3.      1.      3.
      1.     -2.      0.     -1.     -3.     -2.     -2.     -1.     -3.      0.     -3.     -1.     -1.     -4.     -1.      2.      4.
     -7.      1.     -5.     -8.     -8.     -6.     -8.     -8.     -5.     -7.     -5.     -5.     -7.     -1.     -7.     -2.     -6.     12.
     -4.     -6.     -2.     -5.     -1.     -5.     -4.     -6.     -1.     -2.     -3.     -6.     -4.      4.     -6.     -3.     -3.     -1.      8.
      0.     -3.     -3.     -3.     -2.     -3.     -3.     -2.     -3.      3.      1.     -4.      1.     -3.     -2.     -2.      0.     -8.     -3.      5.
//
H BENS940101
D Log-odds scoring matrix collected in 6.4-8.7 PAM (Benner et al., 1994)
R PMID:7700864
A Benner, S.A., Cohen, M.A. and Gonnet, G.H.
T Amino acid substitution during functionally constrained divergent
  evolution of protein sequences
J Protein Engineering 7, 1323-1332 (1994)
* extrapolated to 250 PAM
M rows = ARNDCQEGHILKMFPSTWYV, cols = ARNDCQEGHILKMFPSTWYV
     2.5
    -1.7     5.1
     0.0    -0.1     3.6
    -0.6    -1.5     2.5     5.2
    -1.7    -0.4    -1.6    -3.7    12.1
    -1.7     2.5     0.1     0.6    -3.2     5.3
    -0.7    -0.4     1.1     4.4    -4.7     2.1     5.2
     0.8    -0.1    -0.1     0.8    -1.3    -1.6     0.5     5.8
    -2.1     1.8     1.4     0.1    -1.2     3.2    -0.2    -2.1     6.1
     0.1    -3.8    -2.5    -4.2    -3.6    -3.8    -4.1    -3.4    -3.7     4.4
    -1.3    -3.2    -3.4    -5.3    -3.8    -2.4    -5.0    -4.6    -2.2     2.4     4.8
    -1.9     4.3     1.0    -0.2    -2.8     2.5     0.9    -1.4     0.9    -3.8    -4.1     5.6
    -0.2    -3.0    -2.5    -4.3    -3.7    -3.1    -4.1    -3.7    -3.4     4.0     2.9    -2.9     4.8
    -3.2    -4.9    -3.5    -5.7    -0.1    -4.4    -6.7    -5.7     0.1     0.0     2.4    -6.3    -0.1     8.3
     1.1    -1.3    -1.1    -2.8    -2.7     0.1    -2.6    -1.7    -0.4    -2.0    -0.2    -2.3    -1.8    -3.2     6.5
     1.4    -0.9     1.2    -0.4     0.9    -1.4    -1.2     0.8    -0.9    -1.2    -1.5    -1.2    -1.3    -1.8     1.4     2.1
     1.7    -1.3     0.5    -1.2    -1.5    -1.7    -1.6    -0.5    -1.7     0.7    -0.4    -1.1     0.6    -2.4     0.6     1.5     2.4
    -4.3     2.0    -4.4    -6.3     1.6    -2.6    -5.6    -1.7    -2.8    -5.0    -3.0    -1.4    -4.4    -1.6    -4.8    -2.9    -2.6    14.7
    -4.0    -2.6    -0.9    -2.3     2.6    -1.4    -4.1    -4.9     4.4    -3.3    -1.6    -4.0    -3.6     5.6    -3.8    -1.8    -3.4    -0.3     9.5
     0.7    -3.7    -2.4    -3.3    -3.1    -3.5    -3.0    -2.3    -3.8     3.9     1.9    -3.8     3.3    -0.5    -1.6    -0.9     0.6    -4.8    -3.8     4.0
//
H BENS940102
D Log-odds scoring matrix collected in 22-29 PAM (Benner et al., 1994)
R PMID:7700864
A Benner, S.A., Cohen, M.A. and Gonnet, G.H.
T Amino acid substitution during functionally constrained divergent
  evolution of protein sequences
J Protein Engineering 7, 1323-1332 (1994)
* extrapolated to 250 PAM
M rows = ARNDCQEGHILKMFPSTWYV, cols = ARNDCQEGHILKMFPSTWYV
     2.5
    -1.2     5.0
     0.0     0.4     3.3
    -0.2    -1.0     2.4     4.8
    -1.2    -1.6    -1.9    -3.7    12.6
    -0.9     2.2     0.5     0.6    -3.3     4.2
    -0.3    -0.1     1.2     3.9    -4.3     1.7     4.6
     0.8    -0.7     0.4     0.7    -1.7    -1.4     0.5     6.2
    -1.6     1.5     1.4     0.3    -1.5     2.4    -0.2    -2.0     6.1
    -0.4    -3.2    -2.7    -4.0    -2.4    -2.7    -3.6    -3.8    -3.2     4.2
    -1.7    -2.9    -3.5    -4.9    -2.6    -2.0    -4.4    -4.9    -2.1     2.7     4.6
    -1.0     3.9     1.0     0.2    -3.3     2.2     1.0    -1.0     0.8    -3.0    -3.3     4.4
    -0.8    -2.1    -2.6    -3.9    -2.5    -1.7    -3.4    -3.8    -2.4     3.1     3.2    -2.0     4.9
    -3.1    -4.3    -3.5    -5.4    -0.1    -3.6    -5.7    -5.8     0.3     0.5     2.2    -5.1     0.7     7.7
     0.8    -1.2    -1.1    -1.8    -3.1    -0.1    -1.7    -1.8    -0.4    -2.3    -1.3    -1.6    -2.0    -3.4     7.0
     1.3    -0.5     1.1     0.1     0.3    -0.6    -0.5     0.6    -0.5    -1.4    -2.1    -0.4    -1.5    -2.2     1.1     2.0
     1.4    -0.7     0.5    -0.7    -1.1    -0.7    -0.9    -0.7    -1.1     0.3    -1.0    -0.4     0.1    -2.6     0.4     1.5     2.5
    -5.5    -1.1    -5.2    -6.4     0.5    -3.3    -6.3    -4.5    -2.7    -4.4    -1.8    -3.7    -2.8     0.5    -5.8    -3.9    -4.5    15.7
    -3.5    -2.7    -1.2    -3.0     0.6    -1.9    -4.0    -4.8     3.7    -2.2    -0.7    -3.6    -1.8     5.9    -3.5    -1.9    -3.0     1.5     9.0
     0.4    -2.9    -2.3    -3.0    -1.7    -2.4    -2.7    -2.5    -3.0     3.6     2.0    -2.7     2.5    -0.1    -1.7    -0.9     0.4    -4.5    -2.6     3.7
//
H BENS940103
D Log-odds scoring matrix collected in 74-100 PAM (Benner et al., 1994)
R PMID:7700864
A Benner, S.A., Cohen, M.A. and Gonnet, G.H.
T Amino acid substitution during functionally constrained divergent
  evolution of protein sequences
J Protein Engineering 7, 1323-1332 (1994)
* extrapolated to 250 PAM
M rows = ARNDCQEGHILKMFPSTWYV, cols = ARNDCQEGHILKMFPSTWYV
     2.4
    -0.8     4.8
    -0.2     0.3     3.6
    -0.3    -0.5     2.2     4.8
     0.3    -2.2    -1.8    -3.2    11.8
    -0.3     1.6     0.7     0.8    -2.6     3.0
    -0.1     0.3     1.0     2.9    -3.2     1.7     3.7
     0.6    -1.0     0.4     0.2    -2.0    -1.1    -0.5     6.6
    -1.0     1.0     1.2     0.4    -1.3     1.4     0.2    -1.6     6.1
    -0.8    -2.6    -2.8    -3.9    -1.2    -2.0    -2.9    -4.3    -2.3     4.0
    -1.4    -2.4    -3.1    -4.2    -1.6    -1.7    -3.1    -4.6    -1.9     2.8     4.2
    -0.4     2.9     0.9     0.4    -2.9     1.7     1.2    -1.1     0.6    -2.3    -2.4     3.4
    -0.8    -1.8    -2.2    -3.2    -1.2    -1.0    -2.2    -3.5    -1.5     2.6     2.9    -1.5     4.5
    -2.6    -3.5    -3.2    -4.7    -0.7    -2.8    -4.3    -5.4     0.0     0.9     2.1    -3.6     1.3     7.2
     0.4    -1.0    -1.0    -1.0    -3.1    -0.2    -0.7    -1.7    -1.0    -2.6    -2.2    -0.8    -2.4    -3.8     7.5
     1.1    -0.2     0.9     0.4     0.1     0.1     0.1     0.4    -0.3    -1.8    -2.2     0.0    -1.4    -2.6     0.5     2.1
     0.7    -0.3     0.4    -0.2    -0.6    -0.1    -0.2    -1.0    -0.5    -0.3    -1.1     0.1    -0.4    -2.2     0.1     1.4     2.5
    -4.1    -1.6    -4.0    -5.5    -0.9    -2.8    -4.7    -4.1    -1.0    -2.3    -0.9    -3.6    -1.3     3.0    -5.2    -3.4    -3.7    14.7
    -2.6    -2.0    -1.4    -2.8    -0.4    -1.8    -3.0    -4.3     2.5    -1.0    -0.1    -2.4    -0.5     5.3    -3.4    -1.9    -2.1     3.6     8.1
     0.1    -2.2    -2.2    -2.9    -0.2    -1.7    -2.1    -3.1    -2.1     3.2     1.9    -1.9     1.8     0.1    -1.9    -1.0     0.2    -2.9    -1.4     3.4
//
H BENS940104
D Genetic code matrix (Benner et al., 1994)
R PMID:7700864
A Benner, S.A., Cohen, M.A. and Gonnet, G.H.
T Amino acid substitution during functionally constrained divergent
  evolution of protein sequences
J Protein Engineering 7, 1323-1332 (1994)
* extrapolated to 250 PAM
M rows = ARNDCQEGHILKMFPSTWYV, cols = ARNDCQEGHILKMFPSTWYV
     4.0
    -1.6     2.9
    -1.7    -1.5     4.7
     1.0    -2.3     1.7     4.8
    -1.9     0.7    -1.5    -1.6     5.5
    -2.1     0.3     0.4     0.3    -3.1     5.5
     1.3    -2.0     0.3     3.8    -3.0     2.0     5.7
     1.2     0.8    -2.6     1.1     1.0    -2.1     1.4     4.2
    -2.1     3.6     1.8     1.7    -1.6     3.6     0.3    -2.2     4.7
    -1.8    -1.2     0.9    -2.1    -1.9    -1.9    -2.3    -2.5    -1.8     4.1
    -2.3    -0.4    -2.2    -2.4    -1.3     0.1    -2.5    -2.2    -0.1     1.2     3.4
    -1.9    -0.2     3.5     0.3    -3.2     2.2     2.0    -2.2     0.6     0.7    -2.0     5.6
    -2.0    -0.4     0.1    -2.5    -2.7    -1.2    -1.8    -2.3    -1.8     3.3     1.5     1.6     5.4
    -2.4    -1.5    -1.3    -1.7     1.8    -2.1    -2.9    -1.9    -1.1     1.3     2.2    -2.8     0.5     4.5
     0.8     0.3    -1.6    -2.2    -1.9     1.0    -2.1    -1.8     0.7    -1.6     0.0    -1.5    -1.4    -1.8     3.8
     0.1     0.3    -0.3    -2.1     1.5    -2.3    -2.8    -0.6    -1.6    -0.5    -1.2    -1.5    -1.3     0.0     0.4     2.6
     0.9    -0.6     0.9    -2.1    -1.9    -1.7    -2.1    -2.1    -1.8     0.8    -1.9     1.0     0.7    -2.1     1.1     1.0     4.0
    -2.2     1.8    -3.0    -2.9     4.1    -2.3    -3.2     1.4    -2.1    -2.2    -0.3    -3.0    -2.0     0.0    -1.6     0.8    -2.2     7.5
    -2.4    -1.9     2.5     2.3     2.6    -0.8    -0.9    -1.8     2.3    -1.6    -1.6    -0.8    -2.9     2.0    -2.3     0.3    -2.1    -0.5     6.5
     1.0    -2.1    -2.2     1.0    -2.2    -2.0     1.3     1.1    -2.1     1.0     1.1    -2.1     1.0     1.0    -2.1    -2.2    -2.2    -2.1    -2.2     4.1
//
H CSEM940101
D Residue replace ability matrix (Cserzo et al., 1994)
R PMID:7966267
A Cserzo, M., Bernassau, J.-M., Simon, I. and Maigret, B.
T New alignment strategy for transmembrane proteins
J J. Mol. Biol. 243, 388-396 (1994)
* Diagonal elements are missing.
* We use 1 as diagonal elements.
M rows = ARNDCQEGHILKMFPSTWYV, cols = ARNDCQEGHILKMFPSTWYV
      1.
   -0.07      1.
   -0.14    0.12      1.
   -0.08   -0.01    0.56      1.
    0.04   -0.20   -0.14   -0.24      1.
   -0.01    0.57    0.20    0.19   -0.29      1.
    0.08    0.34    0.13    0.37   -0.51    0.51      1.
    0.11   -0.11    0.22    0.11    0.25   -0.13   -0.23      1.
   -0.11    0.13    0.32    0.22    0.18    0.05   -0.19    0.18      1.
   -0.10   -0.29   -0.37   -0.54    0.26   -0.43   -0.51   -0.22   -0.14      1.
    0.20   -0.20   -0.39   -0.55    0.23   -0.30   -0.45   -0.14   -0.12    0.60      1.
   -0.07    0.47    0.22    0.18   -0.43    0.52    0.54   -0.23   -0.09   -0.40   -0.34      1.
    0.15   -0.17   -0.11   -0.25    0.10   -0.18   -0.14   -0.01   -0.19    0.36    0.38   -0.16      1.
   -0.25   -0.31   -0.33   -0.40    0.30   -0.44   -0.50   -0.09   -0.06    0.60    0.44   -0.41    0.22      1.
   -0.07   -0.17    0.05    0.09    0.02   -0.03   -0.11    0.25    0.05   -0.19   -0.20   -0.17   -0.17   -0.12      1.
    0.14   -0.16    0.14    0.22    0.10   -0.06   -0.17    0.29    0.14   -0.27   -0.19   -0.24   -0.17   -0.01    0.27      1.
    0.11   -0.32    0.13    0.23    0.14   -0.15   -0.27   -0.02    0.08    0.00   -0.04   -0.24   -0.02    0.02    0.20    0.45      1.
   -0.25   -0.03   -0.39   -0.41    0.18   -0.17   -0.22   -0.08   -0.11    0.36    0.22   -0.22    0.16    0.41   -0.13   -0.17   -0.12      1.
   -0.36   -0.03   -0.27   -0.34    0.21   -0.28   -0.32   -0.24    0.08    0.43    0.17   -0.20    0.07    0.54   -0.23   -0.21   -0.14    0.43      1.
    0.06   -0.29   -0.46   -0.48    0.33   -0.38   -0.44   -0.12   -0.18    0.70    0.49   -0.36    0.23    0.47   -0.17   -0.18    0.07    0.29    0.31      1.
//
H DAYM780301
D Log odds matrix for 250 PAMs (Dayhoff et al., 1978)
R
A Dayhoff, M.O., Schwartz, R.M. and Orcutt, B.C.
T A model of evolutionary change in proteins
J 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)
M rows = ARNDCQEGHILKMFPSTWYV, cols = ARNDCQEGHILKMFPSTWYV
      2.
     -2.      6.
      0.      0.      2.
      0.     -1.      2.      4.
     -2.     -4.     -4.     -5.     12.
      0.      1.      1.      2.     -5.      4.
      0.     -1.      1.      3.     -5.      2.      4.
      1.     -3.      0.      1.     -3.     -1.      0.      5.
     -1.      2.      2.      1.     -3.      3.      1.     -2.      6.
     -1.     -2.     -2.     -2.     -2.     -2.     -2.     -3.     -2.      5.
     -2.     -3.     -3.     -4.     -6.     -2.     -3.     -4.     -2.      2.      6.
     -1.      3.      1.      0.     -5.      1.      0.     -2.      0.     -2.     -3.      5.
     -1.      0.     -2.     -3.     -5.     -1.     -2.     -3.     -2.      2.      4.      0.      6.
     -4.     -4.     -4.     -6.     -4.     -5.     -5.     -5.     -2.      1.      2.     -5.      0.      9.
      1.      0.     -1.     -1.     -3.      0.     -1.     -1.      0.     -2.     -3.     -1.     -2.     -5.      6.
      1.      0.      1.      0.      0.     -1.      0.      1.     -1.     -1.     -3.      0.     -2.     -3.      1.      2.
      1.     -1.      0.      0.     -2.     -1.      0.      0.     -1.      0.     -2.      0.     -1.     -3.      0.      1.      3.
     -6.      2.     -4.     -7.     -8.     -5.     -7.     -7.     -3.     -5.     -2.     -3.     -4.      0.     -6.     -2.     -5.     17.
     -3.     -4.     -2.     -4.      0.     -4.     -4.     -5.      0.     -1.     -1.     -4.     -2.      7.     -5.     -3.     -3.      0.     10.
      0.     -2.     -2.     -2.     -2.     -2.     -2.     -1.     -2.      4.      2.     -2.      2.     -1.     -1.     -1.      0.     -6.     -2.      4.
//
H FEND850101
D Structure-Genetic matrix (Feng et al., 1985)
R PMID:6100188
A Feng, D.F., Johnson, M.S. and Doolittle, R.F.
T Aligning amino acid sequences: comparison of commonly used methods
J J. Mol. Evol. 21, 112-125 (1985)
M rows = ARNDCQEGHILKMFPSTWYV, cols = ARNDCQEGHILKMFPSTWYV
      6.
      2.      6.
      3.      2.      6.
      4.      2.      5.      6.
      2.      2.      2.      1.      6.
      3.      3.      3.      4.      1.      6.
      4.      2.      3.      5.      0.      4.      6.
      5.      3.      3.      4.      3.      2.      4.      6.
      2.      4.      4.      3.      2.      4.      2.      1.      6.
      2.      2.      2.      1.      2.      1.      1.      2.      1.      6.
      2.      2.      1.      1.      2.      2.      1.      2.      3.      5.      6.
      3.      5.      4.      3.      0.      4.      4.      2.      3.      2.      2.      6.
      2.      2.      1.      0.      2.      2.      1.      1.      1.      4.      5.      2.      6.
      2.      1.      1.      1.      3.      1.      0.      1.      2.      4.      4.      0.      2.      6.
      5.      3.      2.      2.      2.      3.      3.      3.      3.      2.      3.      2.      2.      2.      6.
      5.      3.      5.      3.      4.      3.      3.      5.      3.      2.      2.      3.      1.      3.      4.      6.
      5.      3.      4.      2.      2.      3.      3.      2.      2.      3.      2.      4.      3.      1.      4.      5.      6.
      2.      2.      0.      0.      3.      1.      1.      3.      1.      2.      4.      1.      3.      3.      2.      2.      1.      6.
      2.      1.      3.      2.      3.      2.      1.      2.      3.      3.      3.      1.      2.      5.      2.      3.      2.      3.      6.
      5.      2.      2.      3.      2.      2.      4.      4.      1.      5.      5.      3.      4.      4.      3.      2.      3.      3.      3.      6.
//
H FITW660101
D Mutation values for the interconversion of amino acid pairs (Fitch, 1966)
R PMID:5917736
A Fitch, W.M.
T An improved method of testing for evolutionary homology
J J. Mol. Biol. 16, 9-16 (1966)
M rows = ARNDCQEGHILKMFPSTWYV, cols = ARNDCQEGHILKMFPSTWYV
      0.
      2.      0.
      2.      2.      0.
      1.      2.      1.      0.
      2.      1.      2.      2.      0.
      2.      1.      2.      2.      2.      0.
      1.      2.      2.      1.      3.      1.      0.
      1.      1.      2.      1.      1.      2.      1.      0.
      2.      1.      1.      1.      2.      1.      2.      2.      0.
      2.      2.      1.      2.      2.      3.      3.      2.      2.      0.
      2.      1.      2.      2.      2.      1.      2.      1.      1.      1.      0.
      2.      1.      1.      2.      3.      1.      1.      2.      2.      2.      2.      0.
      2.      1.      2.      3.      3.      2.      2.      2.      3.      1.      1.      1.      0.
      2.      2.      2.      2.      1.      2.      3.      2.      2.      1.      1.      3.      2.      0.
      1.      1.      2.      2.      2.      1.      2.      2.      1.      2.      1.      2.      2.      2.      0.
      1.      1.      1.      2.      1.      1.      2.      1.      2.      1.      1.      2.      2.      1.      1.      0.
      1.      1.      1.      2.      2.      2.      2.      2.      2.      1.      2.      1.      1.      2.      1.      1.      0.
      2.      1.      3.      3.      1.      1.      2.      1.      3.      3.      1.      2.      2.      2.      2.      1.      2.      0.
      2.      2.      1.      1.      1.      1.      2.      2.      1.      2.      2.      2.      3.      1.      2.      1.      2.      2.      0.
      1.      2.      2.      1.      1.      2.      1.      1.      2.      1.      1.      2.      1.      1.      2.      2.      2.      2.      2.      0.
//
H GEOD900101
D Hydrophobicity scoring matrix (George et al., 1990)
R PMID:2314281
A George, D.G., Barker, W.C. and Hunt, L.T.
T Mutation data matrix and its uses
J Methods Enzymol. 183, 333-351 (1990)
M rows = ARNDCQEGHILKMFPSTWYV, cols = ARNDCQEGHILKMFPSTWYV
     10.
      5.     10.
      9.      6.     10.
      5.      9.      6.     10.
      9.      4.      8.      5.     10.
      9.      6.     10.      6.      8.     10.
      5.      9.      6.     10.      5.      6.     10.
      9.      5.     10.      6.      8.     10.      6.     10.
     10.      5.      9.      5.      9.      9.      5.      9.     10.
      8.      3.      7.      3.      9.      7.      3.      7.      8.     10.
      8.      3.      7.      3.      9.      7.      3.      7.      8.     10.     10.
      5.     10.      6.      9.      4.      6.      9.      5.      5.      3.      3.     10.
      9.      3.      8.      4.     10.      8.      4.      8.      9.      9.      9.      3.     10.
      7.      1.      6.      2.      8.      6.      2.      6.      7.      9.      9.      1.      8.     10.
      9.      3.      8.      4.      9.      8.      4.      8.      9.      9.      9.      3.     10.      8.     10.
      9.      6.     10.      7.      8.     10.      7.     10.      9.      7.      7.      6.      8.      6.      7.     10.
     10.      5.      9.      5.      9.      9.      5.      9.     10.      8.      8.      5.      9.      7.      8.      9.     10.
      5.      0.      4.      1.      6.      4.      1.      5.      5.      8.      8.      0.      7.      9.      7.      4.      5.     10.
      7.      2.      6.      3.      8.      6.      3.      6.      7.      9.      9.      2.      8.     10.      9.      6.      7.      8.     10.
      8.      3.      7.      4.      9.      7.      4.      8.      8.     10.     10.      3.     10.      8.     10.      7.      8.      7.      9.     10.
//
H GONG920101
D The mutation matrix for initially aligning (Gonnet et al., 1992)
R PMID:1604319
A Gonnet, G.H., Cohen, M.A. and Benner, S.A.
T Exhaustive matching of the entire protein sequence database
J Science 256, 1443-1445 (1992)
M rows = ARNDCQEGHILKMFPSTWYV, cols = ARNDCQEGHILKMFPSTWYV
     2.4
    -0.6     4.7
    -0.3     0.3     3.8
    -0.3    -0.3     2.2     4.7
     0.5    -2.2    -1.8    -3.2    11.5
    -0.2     1.5     0.7     0.9    -2.4     2.7
     0.0     0.4     0.9     2.7    -3.0     1.7     3.6
     0.5    -1.0     0.4     0.1    -2.0    -1.0    -0.8     6.6
    -0.8     0.6     1.2     0.4    -1.3     1.2     0.4    -1.4     6.0
    -0.8    -2.4    -2.8    -3.8    -1.1    -1.9    -2.7    -4.5    -2.2     4.0
    -1.2    -2.2    -3.0    -4.0    -1.5    -1.6    -2.8    -4.4    -1.9     2.8     4.0
    -0.4     2.7     0.8     0.5    -2.8     1.5     1.2    -1.1     0.6    -2.1    -2.1     3.2
    -0.7    -1.7    -2.2    -3.0    -0.9    -1.0    -2.0    -3.5    -1.3     2.5     2.8    -1.4     4.3
    -2.3    -3.2    -3.1    -4.5    -0.8    -2.6    -3.9    -5.2    -0.1     1.0     2.0    -3.3     1.6     7.0
     0.3    -0.9    -0.9    -0.7    -3.1    -0.2    -0.5    -1.6    -1.1    -2.6    -2.3    -0.6    -2.4    -3.8     7.6
     1.1    -0.2     0.9     0.5     0.1     0.2     0.2     0.4    -0.2    -1.8    -2.1     0.1    -1.4    -2.8     0.4     2.2
     0.6    -0.2     0.5     0.0    -0.5     0.0    -0.1    -1.1    -0.3    -0.6    -1.3     0.1    -0.6    -2.2     0.1     1.5     2.5
    -3.6    -1.6    -3.6    -5.2    -1.0    -2.7    -4.3    -4.0    -0.8    -1.8    -0.7    -3.5    -1.0     3.6    -5.0    -3.3    -3.5    14.2
    -2.2    -1.8    -1.4    -2.8    -0.5    -1.7    -2.7    -4.0     2.2    -0.7     0.0    -2.1    -0.2     5.1    -3.1    -1.9    -1.9     4.1     7.8
     0.1    -2.0    -2.2    -2.9     0.0    -1.5    -1.9    -3.3    -2.0     3.1     1.8    -1.7     1.6     0.1    -1.8    -1.0     0.0    -2.6    -1.1     3.4
//
H GRAR740104
D Chemical distance (Grantham, 1974)
R PMID:4843792
A Grantham, R.
T Amino acid difference formula to help explain protein evolution
J Science 185, 862-864 (1974)
M rows = ARNDCQEGHILKMFPSTWYV, cols = ARNDCQEGHILKMFPSTWYV
      0.
    112.      0.
    111.     86.      0.
    126.     96.     23.      0.
    195.    180.    139.    154.      0.
     91.     43.     46.     61.    154.      0.
    107.     54.     42.     45.    170.     29.      0.
     60.    125.     80.     94.    159.     87.     98.      0.
     86.     29.     68.     81.    174.     24.     40.     98.      0.
     94.     97.    149.    168.    198.    109.    134.    135.     94.      0.
     96.    102.    153.    172.    198.    113.    138.    138.     99.      5.      0.
    106.     26.     94.    101.    202.     53.     56.    127.     32.    102.    107.      0.
     84.     91.    142.    160.    196.    101.    126.    127.     87.     10.     15.     95.      0.
    113.     97.    158.    177.    205.    116.    140.    153.    100.     21.     22.    102.     28.      0.
     27.    103.     91.    108.    169.     76.     93.     42.     77.     95.     98.    103.     87.    114.      0.
     99.    110.     46.     65.    112.     68.     80.     56.     89.    142.    145.    121.    135.    155.     74.      0.
     58.     71.     65.     85.    149.     42.     65.     59.     47.     89.     92.     78.     81.    103.     38.     58.      0.
    148.    101.    174.    181.    215.    130.    152.    184.    115.     61.     61.    110.     67.     40.    147.    177.    128.      0.
    112.     77.    143.    160.    194.     99.    122.    147.     83.     33.     36.     85.     36.     22.    110.    144.     92.     37.      0.
     64.     96.    133.    152.    192.     96.    121.    109.     84.     29.     32.     97.     21.     50.     68.    124.     69.     88.     55.      0.
//
H HENS920101
D BLOSUM45 substitution matrix (Henikoff-Henikoff, 1992)
R PMID:1438297
A Henikoff, S. and Henikoff, J.G.
T Amino acid substitution matrices from protein blocks
J Proc. Natl. Acad. Sci. USA 89, 10915-10919 (1992)
* matrix in 1/3 Bit Units
M rows = ARNDCQEGHILKMFPSTWYV, cols = ARNDCQEGHILKMFPSTWYV
      5.
     -2.      7.
     -1.      0.      6.
     -2.     -1.      2.      7.
     -1.     -3.     -2.     -3.     12.
     -1.      1.      0.      0.     -3.      6.
     -1.      0.      0.      2.     -3.      2.      6.
      0.     -2.      0.     -1.     -3.     -2.     -2.      7.
     -2.      0.      1.      0.     -3.      1.      0.     -2.     10.
     -1.     -3.     -2.     -4.     -3.     -2.     -3.     -4.     -3.      5.
     -1.     -2.     -3.     -3.     -2.     -2.     -2.     -3.     -2.      2.      5.
     -1.      3.      0.      0.     -3.      1.      1.     -2.     -1.     -3.     -3.      5.
     -1.     -1.     -2.     -3.     -2.      0.     -2.     -2.      0.      2.      2.     -1.      6.
     -2.     -2.     -2.     -4.     -2.     -4.     -3.     -3.     -2.      0.      1.     -3.      0.      8.
     -1.     -2.     -2.     -1.     -4.     -1.      0.     -2.     -2.     -2.     -3.     -1.     -2.     -3.      9.
      1.     -1.      1.      0.     -1.      0.      0.      0.     -1.     -2.     -3.     -1.     -2.     -2.     -1.      4.
      0.     -1.      0.     -1.     -1.     -1.     -1.     -2.     -2.     -1.     -1.     -1.     -1.     -1.     -1.      2.      5.
     -2.     -2.     -4.     -4.     -5.     -2.     -3.     -2.     -3.     -2.     -2.     -2.     -2.      1.     -3.     -4.     -3.     15.
     -2.     -1.     -2.     -2.     -3.     -1.     -2.     -3.      2.      0.      0.     -1.      0.      3.     -3.     -2.     -1.      3.      8.
      0.     -2.     -3.     -3.     -1.     -3.     -3.     -3.     -3.      3.      1.     -2.      1.      0.     -3.     -1.      0.     -3.     -1.      5.
//
H HENS920102
D BLOSUM62 substitution matrix (Henikoff-Henikoff, 1992)
R PMID:1438297
A Henikoff, S. and Henikoff, J.G.
T Amino acid substitution matrices from protein blocks
J Proc. Natl. Acad. Sci. USA 89, 10915-10919 (1992)
* matrix in 1/3 Bit Units
M rows = ARNDCQEGHILKMFPSTWYV, cols = ARNDCQEGHILKMFPSTWYV
      6.
     -2.      8.
     -2.     -1.      8.
     -3.     -2.      2.      9.
     -1.     -5.     -4.     -5.     13.
     -1.      1.      0.      0.     -4.      8.
     -1.      0.      0.      2.     -5.      3.      7.
      0.     -3.     -1.     -2.     -4.     -3.     -3.      8.
     -2.      0.      1.     -2.     -4.      1.      0.     -3.     11.
     -2.     -4.     -5.     -5.     -2.     -4.     -5.     -6.     -5.      6.
     -2.     -3.     -5.     -5.     -2.     -3.     -4.     -5.     -4.      2.      6.
     -1.      3.      0.     -1.     -5.      2.      1.     -2.     -1.     -4.     -4.      7.
     -1.     -2.     -3.     -5.     -2.     -1.     -3.     -4.     -2.      2.      3.     -2.      8.
     -3.     -4.     -4.     -5.     -4.     -5.     -5.     -5.     -2.      0.      1.     -5.      0.      9.
     -1.     -3.     -3.     -2.     -4.     -2.     -2.     -3.     -3.     -4.     -4.     -2.     -4.     -5.     11.
      2.     -1.      1.      0.     -1.      0.      0.      0.     -1.     -4.     -4.      0.     -2.     -4.     -1.      6.
      0.     -2.      0.     -2.     -1.     -1.     -1.     -2.     -3.     -1.     -2.     -1.     -1.     -3.     -2.      2.      7.
     -4.     -4.     -6.     -6.     -3.     -3.     -4.     -4.     -4.     -4.     -2.     -4.     -2.      1.     -5.     -4.     -4.     16.
     -3.     -3.     -3.     -5.     -4.     -2.     -3.     -5.      3.     -2.     -2.     -3.     -1.      4.     -4.     -3.     -2.      3.     10.
      0.     -4.     -4.     -5.     -1.     -3.     -4.     -5.     -5.      4.      1.     -3.      1.     -1.     -4.     -2.      0.     -4.     -2.      6.
//
H HENS920103
D BLOSUM80 substitution matrix (Henikoff-Henikoff, 1992)
R PMID:1438297
A Henikoff, S. and Henikoff, J.G.
T Amino acid substitution matrices from protein blocks
J Proc. Natl. Acad. Sci. USA 89, 10915-10919 (1992)
* matrix in 1/3 Bit Units
M rows = ARNDCQEGHILKMFPSTWYV, cols = ARNDCQEGHILKMFPSTWYV
      7.
     -3.      9.
     -3.     -1.      9.
     -3.     -3.      2.     10.
     -1.     -6.     -5.     -7.     13.
     -2.      1.      0.     -1.     -5.      9.
     -2.     -1.     -1.      2.     -7.      3.      8.
      0.     -4.     -1.     -3.     -6.     -4.     -4.      9.
     -3.      0.      1.     -2.     -7.      1.      0.     -4.     12.
     -3.     -5.     -6.     -7.     -2.     -5.     -6.     -7.     -6.      7.
     -3.     -4.     -6.     -7.     -3.     -4.     -6.     -7.     -5.      2.      6.
     -1.      3.      0.     -2.     -6.      2.      1.     -3.     -1.     -5.     -4.      8.
     -2.     -3.     -4.     -6.     -3.     -1.     -4.     -5.     -4.      2.      3.     -3.      9.
     -4.     -5.     -6.     -6.     -4.     -5.     -6.     -6.     -2.     -1.      0.     -5.      0.     10.
     -1.     -3.     -4.     -3.     -6.     -3.     -2.     -5.     -4.     -5.     -5.     -2.     -4.     -6.     12.
      2.     -2.      1.     -1.     -2.     -1.     -1.     -1.     -2.     -4.     -4.     -1.     -3.     -4.     -2.      7.
      0.     -2.      0.     -2.     -2.     -1.     -2.     -3.     -3.     -2.     -3.     -1.     -1.     -4.     -3.      2.      8.
     -5.     -5.     -7.     -8.     -5.     -4.     -6.     -6.     -4.     -5.     -4.     -6.     -3.      0.     -7.     -6.     -5.     16.
     -4.     -4.     -4.     -6.     -5.     -3.     -5.     -6.      3.     -3.     -2.     -4.     -3.      4.     -6.     -3.     -3.      3.     11.
     -1.     -4.     -5.     -6.     -2.     -4.     -4.     -6.     -5.      4.      1.     -4.      1.     -2.     -4.     -3.      0.     -5.     -3.      7.
//
H JOHM930101
D Structure-based amino acid scoring table (Johnson-Overington, 1993)
R PMID:8411177
A Johnson, M.S. and Overington, J.P.
T A structural basis for sequence comparisons
  An evaluation of scoring methodologies
J J. Mol. Biol. 233, 716-738 (1993)
M rows = ARNDCQEGHILKMFPSTWYV, cols = ARNDCQEGHILKMFPSTWYV
     6.0
    -1.6    10.0
    -1.4    -1.5     8.0
    -1.6    -3.4     2.6     8.5
    -3.4    -5.6    -7.6    -9.7    16.1
    -0.6     2.1    -0.8    -1.1    -6.9     9.0
    -0.7    -0.2    -0.7     2.4    -6.9     2.4     8.6
    -0.5    -2.8    -1.4    -2.1    -8.2    -2.8    -2.5     8.0
    -3.1     0.1     1.7    -0.7    -8.2     1.4    -2.3    -3.2    12.7
    -2.2    -5.4    -4.7    -4.8    -7.7    -7.0    -4.8    -5.5    -5.1     8.1
    -3.3    -3.7    -4.8    -8.0    -8.7    -4.4    -5.6    -7.2    -4.2     2.6     7.3
    -0.9     3.2     0.1    -1.5    -8.7     1.1     1.1    -3.5     0.1    -4.7    -3.4     7.6
    -1.5    -4.2    -3.7    -5.9    -4.4    -0.6    -2.8    -5.2    -2.3     2.6     4.4    -1.9    11.2
    -3.2    -6.0    -3.8    -7.0    -4.4    -6.4    -6.4    -8.6    -1.7     0.5     1.8    -5.6    -0.6    10.4
    -1.0    -3.6    -2.4    -1.0    -8.9    -3.6    -1.5    -2.5    -4.3    -5.7    -2.8    -0.6    -9.8    -5.0    10.3
     0.0    -0.6     1.0    -0.2    -7.7    -1.2    -2.2    -1.3    -2.6    -4.7    -5.2    -1.5    -4.8    -4.8    -1.0     5.8
    -0.8    -1.4     0.1    -1.8    -6.0    -0.4    -0.5    -3.8    -3.0    -3.2    -4.6    -0.2    -3.2    -5.0    -2.0     2.0     6.8
    -5.8    -3.8    -6.1    -6.0    -9.1    -8.2    -7.6    -6.3    -4.0    -3.3    -1.0    -5.4    -0.9     3.4    -7.4    -6.2    -9.3    15.2
    -4.0    -2.1    -1.3    -3.8    -7.7    -5.1    -3.7    -5.4    -0.4    -2.5    -2.4    -3.7    -1.3     3.4    -7.0    -3.4    -2.7     2.3    10.5
    -0.5    -4.9    -5.7    -5.2    -4.8    -3.6    -4.2    -5.6    -3.9     3.9     1.8    -3.7     0.7    -1.3    -5.2    -4.3    -1.9    -4.9    -1.8     7.0
//
H JOND920103
D The 250 PAM PET91 matrix (Jones et al., 1992)
R PMID:1633570
A Jones, D.T., Taylor, W.R. and Thornton, J.M.
T The rapid generation of mutation data matrices from protein sequences
J CABIOS 8, 275-282 (1992)
M rows = ARNDCQEGHILKMFPSTWYV, cols = ARNDCQEGHILKMFPSTWYV
      2.
     -1.      5.
      0.      0.      3.
      0.     -1.      2.      5.
     -1.     -1.     -1.     -3.     11.
     -1.      2.      0.      1.     -3.      5.
     -1.      0.      1.      4.     -4.      2.      5.
      1.      0.      0.      1.     -1.     -1.      0.      5.
     -2.      2.      1.      0.      0.      2.      0.     -2.      6.
      0.     -3.     -2.     -3.     -2.     -3.     -3.     -3.     -3.      4.
     -1.     -3.     -3.     -4.     -3.     -2.     -4.     -4.     -2.      2.      5.
     -1.      4.      1.      0.     -3.      2.      1.     -1.      1.     -3.     -3.      5.
     -1.     -2.     -2.     -3.     -2.     -2.     -3.     -3.     -2.      3.      3.     -2.      6.
     -3.     -4.     -3.     -5.      0.     -4.     -5.     -5.      0.      0.      2.     -5.      0.      8.
      1.     -1.     -1.     -2.     -2.      0.     -2.     -1.      0.     -2.      0.     -2.     -2.     -3.      6.
      1.     -1.      1.      0.      1.     -1.     -1.      1.     -1.     -1.     -2.     -1.     -1.     -2.      1.      2.
      2.     -1.      1.     -1.     -1.     -1.     -1.     -1.     -1.      1.     -1.     -1.      0.     -2.      1.      1.      2.
     -4.      0.     -5.     -5.      1.     -3.     -5.     -2.     -3.     -4.     -2.     -3.     -3.     -1.     -4.     -3.     -4.     15.
     -3.     -2.     -1.     -2.      2.     -2.     -4.     -4.      4.     -2.     -1.     -3.     -2.      5.     -3.     -1.     -3.      0.      9.
      1.     -3.     -2.     -2.     -2.     -3.     -2.     -2.     -3.      4.      2.     -3.      2.      0.     -1.     -1.      0.     -3.     -3.      4.
//
H JOND940101
D The 250 PAM transmembrane protein exchange matrix (Jones et al., 1994)
R PMID:8112466
A Jones, D.T., Taylor, W.R. and Thornton, J.M.
T A mutation data matrix for transmembrane proteins
J FEBS Lett. 339, 269-275 (1994)
M rows = ARNDCQEGHILKMFPSTWYV, cols = ARNDCQEGHILKMFPSTWYV
      2.
     -1.      7.
     -1.      2.     11.
      0.      1.      6.     12.
      0.     -1.     -1.     -3.      6.
     -2.      6.      3.      2.     -3.     11.
      0.      2.      1.      8.     -3.      7.     13.
      1.      0.     -2.      3.     -1.     -1.      3.      6.
     -3.      5.      3.      3.     -1.      7.      2.     -3.     11.
      0.     -3.     -3.     -3.     -1.     -4.     -4.     -2.     -4.      2.
     -2.     -3.     -4.     -5.     -1.     -2.     -5.     -4.     -4.      1.      3.
     -2.      9.      5.      3.     -3.      6.      1.     -1.      4.     -4.     -4.     12.
     -1.      0.     -2.     -3.     -1.     -2.     -3.     -3.     -3.      1.      1.     -1.      3.
     -2.     -4.     -4.     -6.      1.     -4.     -6.     -4.     -3.     -1.      1.     -5.      0.      5.
      0.     -3.     -2.     -2.     -4.      0.     -3.     -2.     -4.     -3.     -1.     -4.     -3.     -4.     11.
      2.     -1.      2.      0.      1.     -1.      0.      1.     -2.     -1.     -2.     -1.     -2.     -1.     -1.      3.
      1.     -1.      1.      0.      0.     -2.     -1.      0.     -2.      0.     -1.     -2.      0.     -2.     -1.      2.      3.
     -4.      5.     -3.     -4.      1.      0.     -3.     -2.     -1.     -3.     -2.      3.     -2.     -3.     -6.     -3.     -4.     12.
     -3.     -1.     -1.     -2.      3.      0.     -5.     -5.      6.     -4.     -3.      1.     -3.      2.     -5.      0.     -3.     -2.     10.
      0.     -2.     -3.     -3.      0.     -4.     -2.     -1.     -4.      2.      0.     -4.      1.     -1.     -3.     -1.      0.     -2.     -4.      2.
//
H KOLA920101
D Conformational similarity weight matrix (Kolaskar-Kulkarni-Kale, 1992)
R PMID:1538389
A Kolaskar, A.S. and Kulkarni-Kale, U.
T Sequence alignment approach to pick up conformationally similar
  protein fragments
J J. Mol. Biol. 223, 1053-1061 (1992)
M rows = ARNDCQEGHILKMFPSTWYV, cols = ARNDCQEGHILKMFPSTWYV
     10.
     6.6     10.
      0.      0.     10.
      0.      0.      9.     10.
      0.      0.      0.      0.     10.
     6.6      9.      0.      0.      0.     10.
      9.     6.6      0.      0.      0.     6.6     10.
      0.      0.      0.      0.      0.      0.      0.     10.
      0.      5.      5.     6.6      9.      5.      0.      0.     10.
      0.      0.      0.      0.      0.      0.      0.      0.      0.     10.
      5.     6.6      0.      0.      0.      9.      5.      0.      0.      0.     10.
     6.6      9.      0.      5.      0.      9.      9.      0.      0.      0.      9.     10.
      5.      9.      0.      0.      0.      5.      0.      0.      0.      0.     6.6      5.     10.
      0.      9.      0.      0.      5.     6.6      0.      0.      5.      0.      5.      5.     6.6     10.
      0.      0.      0.      0.      0.      0.      0.      0.      0.      0.      0.      0.      0.      0.     10.
      0.      5.     6.6     6.6      9.      0.      0.      0.      9.      0.      0.      5.      0.      5.      0.     10.
      0.      5.      0.      0.     6.6      5.      0.      0.      5.      0.      0.      5.      0.      5.      0.     6.6     10.
      0.     6.6      0.      0.      5.      5.      0.      0.      5.      0.      5.      0.     6.6      9.      0.      5.      5.     10.
      0.      5.      0.      0.      5.      5.      0.      0.     6.6      0.      0.      0.      0.      9.      0.     6.6      9.      5.     10.
      0.      0.      0.      0.      0.      0.      0.      0.      0.      9.      0.      0.      0.      0.      0.      0.      0.      0.      0.     10.
//
H LEVJ860101
D The secondary structure similarity matrix (Levin et al., 1986)
R PMID:3743779
A Levin, J.M., Robson, B. and Garnier, J.
T An algorithm for secondary structure determination in proteins based on
  sequence similarity
J FEBS Lett. 205, 303-308 (1986)
M rows = ARNDCQEGHILKMFPSTWYV, cols = ARNDCQEGHILKMFPSTWYV
      2.
      0.      2.
      0.      0.      3.
      0.      0.      1.      2.
      0.      0.      0.      0.      2.
      0.      0.      1.      0.      0.      2.
      1.      0.      0.      1.      0.      1.      2.
      0.      0.      0.      0.      0.      0.      0.      2.
      0.      0.      0.      0.      0.      0.      0.      0.      2.
      0.     -1.     -1.     -1.      0.     -1.     -1.     -1.     -1.      2.
      0.     -1.     -1.     -1.      0.     -1.     -1.     -1.     -1.      0.      2.
      0.      1.      1.      0.      0.      0.      0.      0.      0.     -1.     -1.      2.
      0.     -1.     -1.     -1.      0.     -1.     -1.     -1.     -1.      0.      2.     -1.      2.
     -1.     -1.     -1.     -1.     -1.     -1.     -1.     -1.     -1.      1.      0.     -1.      0.      2.
     -1.      0.      0.      0.      0.      0.     -1.      0.      0.     -1.     -1.      0.     -1.     -1.      3.
      1.      0.      0.      0.      0.      0.      0.      0.      0.     -1.     -1.      0.     -1.     -1.      0.      2.
      0.      0.      0.      0.      0.      0.      0.      0.      0.      0.      0.      0.      0.     -1.      0.      0.      2.
     -1.      0.     -1.     -1.     -1.     -1.     -1.     -1.     -1.      0.      0.     -1.      0.      0.     -1.     -1.     -1.      2.
     -1.     -1.     -1.     -1.     -1.     -1.     -1.     -1.      0.      0.      0.     -1.      0.      1.     -1.     -1.     -1.      0.      2.
      0.     -1.     -1.     -1.      0.     -1.     -1.     -1.     -1.      1.      1.     -1.      0.      0.     -1.     -1.      0.      0.      0.      2.
//
H LUTR910101
D Structure-based comparison table for outside other class (Luthy et al., 1991)
R PMID:1881879
A Luthy, R., McLachlan, A.D. and Eisenberg, D.
T Secondary structure-based profiles: Use of structure-conserving scoring
  tables in searching protein sequence databases for structural similarities
J Proteins 10, 229-239 (1991)
M rows = ARNDCQEGHILKMFPSTWYV, cols = ARNDCQEGHILKMFPSTWYV
     11.
      0.     32.
      2.      2.     11.
      1.     -2.      4.     29.
     -5.     -6.     -7.    -13.    109.
      2.      6.      3.      2.    -10.     16.
      3.      2.      2.      6.    -12.      5.     15.
     -5.     -7.     -4.     -7.    -15.     -8.     -6.     39.
     -4.     -1.      2.     -5.    -23.      2.     -3.    -13.     54.
      1.     -4.     -3.     -7.    -13.     -3.     -3.    -16.    -10.     50.
      1.     -4.     -4.    -10.     -1.     -2.     -4.    -17.     -6.     19.     45.
     -1.      6.     -1.     -2.    -16.      5.      3.    -15.     -8.    -10.    -11.     39.
      1.      0.     -1.     -7.     -3.      0.     -4.    -11.     -3.     20.     24.     -8.     40.
    -13.    -14.    -11.    -15.    -12.    -15.    -18.    -24.     -6.      7.     11.    -26.     13.     85.
      1.     -9.     -8.     -9.    -28.     -6.     -3.    -19.    -12.    -11.    -10.     -9.    -11.    -24.     55.
      4.      1.      3.      2.    -10.      2.      2.     -6.     -4.     -5.     -5.     -1.     -4.    -14.     -3.     17.
      3.     -1.      2.     -2.     -7.      1.      1.    -12.     -5.      0.     -4.     -3.     -2.    -13.     -6.      4.     30.
     -6.      3.     -6.    -10.     -3.    -13.    -14.    -12.     -3.      1.      1.    -19.      9.     10.    -11.     -7.    -14.    124.
     -6.     -3.     -4.    -10.      3.     -9.    -10.    -16.      2.     -3.      2.    -16.      4.     22.    -17.     -6.     -9.     29.     64.
      3.     -3.     -3.     -7.     -7.     -2.     -2.    -12.     -9.     24.     13.     -9.     14.      0.     -8.     -4.     -1.     -1.     -2.     39.
//
H LUTR910102
D Structure-based comparison table for inside other class (Luthy et al., 1991)
R PMID:1881879
A Luthy, R., McLachlan, A.D. and Eisenberg, D.
T Secondary structure-based profiles: Use of structure-conserving scoring
  tables in searching protein sequence databases for structural similarities
J Proteins 10, 229-239 (1991)
M rows = ARNDCQEGHILKMFPSTWYV, cols = ARNDCQEGHILKMFPSTWYV
     12.
      5.      9.
      5.      5.      6.
      6.      8.      8.     17.
      1.    -10.    -11.    -14.     93.
      6.      6.      6.      8.     -5.      7.
      7.      8.      8.     12.    -16.      9.     15.
      5.     -2.      5.      6.    -36.      3.      8.     52.
     -2.      5.      6.      5.    -20.      4.     -3.    -14.     65.
     -1.     -4.     -3.     -6.    -17.     -4.     -5.    -20.    -10.     31.
    -10.    -10.    -10.    -16.    -35.    -12.    -14.    -32.    -18.      9.     37.
      6.     10.     10.     13.    -22.     10.     13.      2.      6.     -5.    -15.     31.
     -6.     -6.     -8.    -13.    -17.     -5.    -12.    -32.     -5.     18.     13.    -11.     61.
    -24.    -11.    -19.    -25.    -36.    -20.    -30.    -52.    -10.     -4.      2.    -30.      2.     67.
     -5.    -12.    -11.     -7.    -30.     -7.     -7.    -11.    -23.    -28.    -36.     -5.    -25.    -28.     83.
      9.      6.      8.      8.    -11.      8.      9.      7.     -1.    -11.    -25.      8.    -18.    -37.     -9.     36.
      8.      6.      6.      8.      1.      8.     10.      0.     -5.     -1.    -18.      6.     -9.    -37.    -14.     10.     35.
    -20.      2.     -6.    -16.      0.     -2.    -18.    -23.    -21.    -19.    -18.    -21.    -20.     11.    -47.    -29.    -29.    129.
     -4.      3.      0.      0.     -7.      0.     -3.    -16.      5.      0.     -2.     -1.      1.     21.    -20.     -6.     -8.     44.     26.
      0.     -3.     -3.     -4.    -12.     -3.     -4.    -20.     -6.     17.      8.     -4.     12.     -9.    -20.    -10.     -2.     -8.     -2.     26.
//
H LUTR910103
D Structure-based comparison table for outside alpha class (Luthy et al., 1991)
R PMID:1881879
A Luthy, R., McLachlan, A.D. and Eisenberg, D.
T Secondary structure-based profiles: Use of structure-conserving scoring
  tables in searching protein sequence databases for structural similarities
J Proteins 10, 229-239 (1991)
M rows = ARNDCQEGHILKMFPSTWYV, cols = ARNDCQEGHILKMFPSTWYV
     24.
     -2.     18.
     -1.      2.     16.
     -2.      0.      4.     23.
      2.      2.      1.     -1.      9.
     -1.      2.      2.      3.      2.     13.
     -2.     -1.      1.      6.     -3.      3.     24.
      1.      2.      4.      2.      4.      2.      1.     29.
     -5.      0.      3.      1.      0.      2.     -1.      0.     43.
     -5.     -3.     -6.     -9.      4.     -4.    -10.     -5.     -4.     41.
    -18.     -7.    -12.    -18.     -3.    -13.    -16.    -15.    -12.     13.     54.
    -10.      5.     -2.     -4.     -4.     -1.     -4.     -4.     -6.    -11.    -21.     32.
     -3.      0.     -5.     -7.      4.      0.     -5.     -5.     -5.     17.     13.     -7.     44.
    -20.    -18.    -18.    -18.      4.    -13.    -24.    -21.     -9.     10.     12.    -30.     13.     99.
     -2.     -2.     -2.      1.     -1.      1.     -1.      0.     -7.     -8.    -24.     -8.    -10.    -32.     67.
      1.      2.      4.      3.      5.      2.      1.      5.      0.     -4.    -12.     -3.     -3.    -18.      1.     17.
      1.      2.      3.      1.      4.      2.      0.      3.      1.      3.     -6.     -3.      2.    -16.     -3.      4.     16.
    -20.     -8.    -18.    -12.     16.     -3.    -16.    -21.      7.    -14.     -3.    -31.    -14.     36.    -29.    -19.     -2.    170.
    -21.    -10.    -10.    -14.     -7.    -12.    -21.    -14.     -1.    -14.    -13.    -25.    -19.     40.    -17.    -16.    -15.     47.    105.
     -5.     -3.     -6.     -4.      5.     -5.     -6.     -5.     -8.     18.     -1.    -11.      7.    -11.     -6.     -2.      3.     -9.    -18.     44.
//
H LUTR910104
D Structure-based comparison table for inside alpha class (Luthy et al., 1991)
R PMID:1881879
A Luthy, R., McLachlan, A.D. and Eisenberg, D.
T Secondary structure-based profiles: Use of structure-conserving scoring
  tables in searching protein sequence databases for structural similarities
J Proteins 10, 229-239 (1991)
M rows = ARNDCQEGHILKMFPSTWYV, cols = ARNDCQEGHILKMFPSTWYV
     22.
     -2.     38.
      4.      5.      4.
     -1.      5.     11.     71.
      8.     -1.      4.    -13.     50.
      2.      9.      4.     10.      0.      6.
      4.     12.      5.     20.     -2.      7.     12.
      5.      0.      7.      0.      3.      5.      8.     53.
    -30.      4.     -3.      7.    -30.     13.     -3.    -32.     95.
     -2.     -1.      0.    -13.      3.      0.     -2.     -6.    -17.     17.
    -14.     -3.     -6.    -20.    -11.     -7.    -10.    -21.    -10.      0.     25.
      1.     22.      6.      9.     -2.      9.     14.      2.     -9.     -1.     -8.     33.
     -2.      2.      0.    -11.      0.     -1.     -3.     -6.     -8.      3.      2.     -3.     17.
    -18.    -14.    -15.    -26.    -12.    -14.    -21.    -25.     -7.     -4.     -4.    -23.      1.     58.
      5.      2.      2.      5.      2.      2.      4.      6.    -14.      1.     -7.      3.     -1.     -8.      4.
      9.      4.      4.      3.     10.      4.      5.      7.    -19.      1.    -10.      5.      0.    -14.      9.     23.
      6.      3.      3.      1.      8.      3.      4.      4.    -16.      2.     -6.      5.      1.    -13.      4.      9.     10.
    -50.    -35.    -34.    -55.    -45.    -15.    -40.    -57.    -41.    -27.    -30.    -23.    -12.      4.    -33.    -45.    -39.    130.
    -15.     -3.     -4.     -8.     -8.      0.     -8.    -17.     23.     -4.     -5.    -13.     -2.     25.     -3.    -10.     -9.     31.     68.
     -1.     -3.     -1.    -15.      1.     -2.     -3.    -10.    -27.      5.     -6.     -4.      3.     -9.      0.     -1.      2.    -23.    -14.     21.
//
H LUTR910105
D Structure-based comparison table for outside beta class (Luthy et al., 1991)
R PMID:1881879
A Luthy, R., McLachlan, A.D. and Eisenberg, D.
T Secondary structure-based profiles: Use of structure-conserving scoring
  tables in searching protein sequence databases for structural similarities
J Proteins 10, 229-239 (1991)
M rows = ARNDCQEGHILKMFPSTWYV, cols = ARNDCQEGHILKMFPSTWYV
     27.
     -3.     32.
     -2.      0.     18.
     -4.      0.      9.     38.
    -22.    -28.      6.    -26.    156.
     -3.      2.      1.      3.    -29.     30.
     -3.     -1.      0.     10.    -30.      6.     25.
      9.      6.     -4.      3.    -33.      3.      4.     59.
    -11.     -7.     14.     12.    -33.      4.     -5.     -4.     84.
     -2.     -2.     -8.    -10.    -26.     -7.     -7.     -8.    -13.     29.
     -7.     -8.    -11.    -21.    -34.    -13.    -13.    -21.     -9.     16.     42.
     -6.      9.     -1.     -2.    -32.      4.      2.     -1.    -19.     -9.    -14.     30.
      2.      2.     -3.     -7.    -17.     -5.     -5.     -2.    -11.     10.     12.     -5.      7.
     -4.     -9.     -8.    -17.     12.     -9.    -12.    -10.     -3.      7.      6.    -11.      2.     47.
      6.     -1.      5.     -2.    -22.      1.    -10.    -10.     -9.      8.      3.    -12.      6.      2.     56.
      5.     -4.      0.      0.      6.     -6.     -3.      0.    -11.    -10.    -15.     -4.     -2.     -9.     -4.     25.
      3.      2.     -4.     -1.     -7.      2.      0.     -1.    -19.     -3.    -12.     -1.      2.     -8.     -2.      4.     20.
     -2.    -31.    -30.    -40.    -34.    -34.    -35.    -33.    -36.    -25.    -29.    -14.    -21.     32.    -25.    -13.    -31.    150.
    -10.    -13.     -2.    -13.    -25.    -14.    -13.    -14.     18.    -10.     -1.    -14.     -4.     24.      3.     -7.    -16.     11.     56.
     -2.     -4.     -9.    -13.    -11.     -8.     -8.    -14.    -19.     11.      8.     -8.      7.     -3.      1.     -7.     -1.    -15.    -13.     24.
//
H LUTR910106
D Structure-based comparison table for inside beta class (Luthy et al., 1991)
R PMID:1881879
A Luthy, R., McLachlan, A.D. and Eisenberg, D.
T Secondary structure-based profiles: Use of structure-conserving scoring
  tables in searching protein sequence databases for structural similarities
J Proteins 10, 229-239 (1991)
M rows = ARNDCQEGHILKMFPSTWYV, cols = ARNDCQEGHILKMFPSTWYV
     18.
      1.     60.
      6.     10.     18.
      4.     -1.     18.     80.
      0.     -7.      5.      0.     66.
      6.     24.     18.     18.      7.     42.
      8.     -1.     22.     29.     -1.     15.     59.
     14.     -8.      6.     -4.    -10.      4.     13.     48.
      2.     11.     13.     24.     -2.     13.     16.     -3.     18.
     -8.    -14.    -14.    -22.    -29.    -14.    -18.     -9.    -15.     20.
     -6.    -12.    -15.    -27.    -29.     -9.    -21.     -9.    -15.     11.     25.
      4.     22.     16.     30.      2.     22.     10.     -2.     14.    -13.    -11.     35.
      1.      3.      3.      5.    -23.      4.      5.      4.      3.      3.      2.      6.     35.
    -12.    -10.     -6.    -24.    -40.    -16.     -7.    -17.      6.    -10.     -4.    -14.     -2.     58.
      4.    -20.    -13.    -26.     -8.    -17.    -19.    -14.    -15.     -9.     -3.    -16.    -16.     -9.     95.
     12.      3.     13.     17.     -1.     10.     13.     16.     10.    -12.    -15.     11.     -2.    -16.     -4.     28.
      6.     10.      8.      2.    -11.      4.      9.      8.      5.     -7.    -11.      7.      3.    -17.     -1.     12.     24.
    -23.     16.    -11.    -24.    -43.    -14.    -19.    -32.     18.     -8.     -8.    -11.    -15.      3.    -32.    -21.     -7.    115.
      0.      7.     13.      7.     -9.      9.     14.     -9.     20.    -16.    -12.     11.      2.     16.     -7.      3.      1.     15.     37.
     -7.    -11.    -17.    -30.    -28.    -15.    -24.     -9.    -19.     11.      9.    -12.     -5.    -13.     -9.    -14.     -7.    -15.    -18.     21.
//
H LUTR910107
D Structure-based comparison table for other class (Luthy et al., 1991)
R PMID:1881879
A Luthy, R., McLachlan, A.D. and Eisenberg, D.
T Secondary structure-based profiles: Use of structure-conserving scoring
  tables in searching protein sequence databases for structural similarities
J Proteins 10, 229-239 (1991)
M rows = ARNDCQEGHILKMFPSTWYV, cols = ARNDCQEGHILKMFPSTWYV
     11.
      1.     28.
      2.      3.     10.
      2.      1.      5.     27.
     -5.     -9.     -9.    -15.    108.
      3.      7.      4.      4.    -11.     14.
      3.      3.      3.      8.    -15.      6.     15.
     -4.     -6.     -2.     -5.    -21.     -6.     -4.     41.
     -3.      0.      2.     -3.    -23.      2.     -2.    -12.     55.
     -1.     -6.     -4.     -9.    -13.     -4.     -5.    -18.    -12.     49.
     -3.     -7.     -7.    -14.    -10.     -6.     -8.    -22.    -10.     19.     48.
      1.      7.      2.      1.    -19.      6.      5.    -12.     -6.    -11.    -15.     38.
     -1.     -2.     -3.     -9.     -7.     -2.     -7.    -15.     -4.     22.     24.    -10.     52.
    -16.    -15.    -14.    -20.    -19.    -18.    -22.    -30.     -9.      5.     10.    -29.     11.     83.
      0.     -8.     -7.     -8.    -30.     -6.     -3.    -17.    -12.    -15.    -16.     -8.    -15.    -26.     58.
      4.      2.      4.      3.    -11.      3.      3.     -4.     -3.     -8.    -10.      1.     -7.    -19.     -3.     19.
      3.      0.      3.     -1.     -6.      2.      2.    -10.     -5.     -1.     -9.     -2.     -4.    -19.     -7.      5.     31.
     -9.      2.     -7.    -13.     -1.    -13.    -17.    -15.     -7.     -5.     -5.    -21.      4.     10.    -16.    -11.    -18.    129.
     -5.     -1.     -2.     -7.      0.     -6.     -9.    -16.      3.     -2.      0.    -12.      3.     22.    -16.     -5.     -9.     35.     59.
      2.     -4.     -4.     -7.     -8.     -3.     -3.    -14.     -9.     24.     14.     -9.     15.     -2.    -11.     -6.     -2.     -3.     -3.     37.
//
H LUTR910108
D Structure-based comparison table for alpha helix class (Luthy et al., 1991)
R PMID:1881879
A Luthy, R., McLachlan, A.D. and Eisenberg, D.
T Secondary structure-based profiles: Use of structure-conserving scoring
  tables in searching protein sequence databases for structural similarities
J Proteins 10, 229-239 (1991)
M rows = ARNDCQEGHILKMFPSTWYV, cols = ARNDCQEGHILKMFPSTWYV
     23.
     -1.     19.
      1.      5.     13.
      0.      3.      7.     28.
      4.      1.      1.     -4.     51.
      1.      5.      5.      6.      1.     11.
      0.      4.      5.     10.     -5.      7.     23.
      2.      3.      6.      4.      4.      3.      3.     37.
     -6.      2.      5.      3.     -5.      4.      1.     -1.     52.
     -6.     -6.     -7.    -12.      5.     -6.    -10.     -8.     -9.     38.
    -19.    -10.    -14.    -21.     -8.    -14.    -18.    -19.    -14.      7.     45.
     -6.      9.      3.      2.     -6.      4.      3.     -1.     -2.    -12.    -21.     34.
     -4.     -2.     -5.     -9.      3.     -2.     -7.     -6.     -7.     12.      8.     -8.     40.
    -23.    -22.    -22.    -24.     -4.    -19.    -28.    -26.    -13.      3.      4.    -34.      8.     88.
      1.      2.      3.      5.     -2.      5.      6.      3.     -4.     -7.    -21.     -1.     -8.    -28.     59.
      3.      4.      5.      5.      7.      4.      4.      6.      0.     -5.    -15.      1.     -4.    -21.      6.     17.
      2.      2.      4.      2.      6.      3.      2.      4.      0.      1.     -9.      0.      0.    -19.      1.      5.     14.
    -43.    -29.    -38.    -35.    -13.    -19.    -38.    -46.    -17.    -25.    -22.    -43.    -11.     19.    -46.    -41.    -25.    162.
    -19.     -8.     -7.    -12.     -8.     -8.    -16.    -14.      4.    -11.    -12.    -20.    -12.     33.    -10.    -14.    -13.     36.     97.
     -6.     -6.     -8.     -9.      3.     -7.     -8.     -9.    -14.     13.     -4.    -13.      6.     -9.     -7.     -4.      1.    -18.    -19.     40.
//
H LUTR910109
D Structure-based comparison table for beta strand class (Luthy et al., 1991)
R PMID:1881879
A Luthy, R., McLachlan, A.D. and Eisenberg, D.
T Secondary structure-based profiles: Use of structure-conserving scoring
  tables in searching protein sequence databases for structural similarities
J Proteins 10, 229-239 (1991)
M rows = ARNDCQEGHILKMFPSTWYV, cols = ARNDCQEGHILKMFPSTWYV
     23.
     -2.     40.
      1.      4.     15.
     -1.      2.     13.     49.
     -5.    -19.     -5.    -16.     97.
      0.      9.      7.      9.    -11.     31.
      0.      2.      8.     17.    -21.     11.     31.
     12.      2.      0.      1.    -18.      4.      6.     54.
     -4.      2.     13.     17.    -12.      8.      5.     -5.     55.
     -7.     -9.    -12.    -17.    -30.    -13.    -13.    -11.    -15.     28.
     -7.    -10.    -13.    -22.    -34.    -12.    -14.    -15.    -13.     13.     34.
     -3.     14.      7.      8.    -23.     12.     10.      0.     -1.    -14.    -13.     34.
      1.      2.     -2.     -5.    -28.     -3.     -3.      2.     -3.      8.      8.     -4.     25.
     -9.    -11.     -9.    -21.    -31.    -12.    -13.    -15.      3.     -3.      1.    -14.     -1.     57.
      5.     -6.      2.     -7.    -12.     -2.    -13.    -13.    -10.     -1.     -1.    -14.      0.     -4.     78.
      7.      1.      6.      8.    -10.      2.      5.      8.      3.    -13.    -15.      4.     -3.    -14.     -4.     26.
      4.      6.      2.      2.    -18.      4.      4.      3.     -4.     -7.    -12.      4.      2.    -13.     -3.      8.     21.
    -17.     -5.    -22.    -32.    -53.    -26.    -29.    -33.      7.    -12.    -15.    -15.    -20.     16.    -28.    -19.    -20.    133.
     -5.     -5.      4.     -5.    -19.     -4.     -3.    -13.     21.    -15.     -7.     -5.     -3.     20.     -1.     -3.     -8.     13.     47.
     -5.     -7.    -12.    -18.    -27.    -11.    -12.    -12.    -18.     11.      8.    -10.      2.     -9.     -4.    -10.     -4.    -17.    -15.     23.
//
H MCLA710101
D The similarity of pairs of amino acids (McLachlan, 1971)
R PMID:5167087
A McLachlan, A.D.
T Tests for comparing related amino-acid sequences
  cytochrome c and cytochrome c551
J J. Mol. Biol. 61, 409-424 (1971)
* (RR 9.)
M rows = ARNDCQEGHILKMFPSTWYV, cols = ARNDCQEGHILKMFPSTWYV
      8.
      2.      8.
      3.      3.      8.
      3.      1.      5.      8.
      1.      1.      1.      1.      9.
      3.      5.      4.      4.      0.      8.
      4.      3.      4.      5.      0.      5.      8.
      3.      3.      3.      3.      1.      2.      3.      8.
      3.      5.      4.      4.      3.      4.      2.      2.      8.
      2.      1.      1.      0.      1.      0.      1.      1.      2.      8.
      2.      2.      1.      1.      0.      3.      1.      1.      2.      5.      8.
      3.      5.      4.      3.      0.      4.      4.      3.      4.      1.      2.      8.
      3.      1.      2.      2.      3.      3.      1.      1.      3.      5.      6.      1.      8.
      1.      1.      0.      1.      0.      0.      0.      0.      4.      3.      5.      0.      5.      9.
      4.      3.      1.      3.      0.      3.      4.      3.      3.      1.      1.      3.      1.      1.      8.
      4.      4.      5.      3.      2.      4.      4.      3.      3.      2.      2.      3.      2.      2.      3.      8.
      3.      3.      3.      3.      2.      3.      4.      2.      4.      3.      3.      3.      3.      1.      3.      5.      8.
      1.      3.      0.      0.      2.      2.      1.      1.      3.      3.      3.      1.      1.      6.      0.      3.      2.      9.
      1.      2.      2.      1.      1.      1.      2.      0.      4.      3.      3.      1.      2.      6.      0.      3.      1.      6.      9.
      3.      2.      1.      1.      1.      2.      2.      2.      2.      5.      5.      2.      4.      3.      2.      2.      3.      2.      3.      8.
//
H MCLA720101
D Chemical similarity scores (McLachlan, 1972)
R PMID:5023183
A McLachlan, A.D.
T Repeating sequences and gene duplication in proteins
J J. Mol. Biol. 64, 417-437 (1972)
M rows = ARNDCQEGHILKMFPSTWYV, cols = ARNDCQEGHILKMFPSTWYV
      5.
      0.      6.
      0.      0.      5.
      0.      0.      3.      5.
      0.      0.      0.      0.      6.
      0.      0.      2.      1.      0.      5.
      0.      0.      1.      2.      0.      3.      5.
      3.      0.      0.      0.      0.      0.      0.      6.
      0.      0.      1.      0.      0.      2.      0.      0.      6.
      0.      0.      0.      0.      0.      0.      0.      0.      0.      5.
      0.      0.      0.      0.      0.      0.      0.      0.      0.      3.      5.
      0.      3.      0.      0.      0.      1.      0.      0.      0.      0.      0.      5.
      0.      0.      0.      0.      0.      0.      0.      0.      0.      3.      3.      0.      6.
      0.      0.      0.      0.      0.      0.      0.      0.      2.      1.      2.      0.      2.      6.
      1.      0.      0.      0.      0.      0.      0.      0.      0.      0.      1.      0.      0.      0.      5.
      1.      0.      1.      0.      2.      1.      0.      0.      0.      0.      0.      0.      0.      0.      0.      5.
      1.      0.      1.      0.      0.      0.      0.      0.      0.      1.      0.      0.      0.      0.      1.      3.      5.
      0.      0.      0.      0.      0.      0.      0.      0.      1.      1.      1.      0.      1.      3.      0.      0.      0.      6.
      0.      0.      0.      0.      0.      0.      0.      0.      2.      1.      1.      0.      1.      3.      0.      0.      0.      2.      6.
      0.      0.      0.      0.      0.      0.      0.      0.      0.      2.      1.      0.      1.      1.      1.      0.      0.      0.      0.      5.
//
H MIYS930101
D Base-substitution-protein-stability matrix (Miyazawa-Jernigan, 1993)
R PMID:8506261
A Miyazawa, S. and Jernigan, R.L.
T A new substitution matrix for protein sequence searches based on
  contact frequencies in protein structures
J Protein Engineering 6, 267-278 (1993)
M rows = ARNDCQEGHILKMFPSTWYV, cols = ARNDCQEGHILKMFPSTWYV
    0.34
   -0.08    0.65
   -0.16    0.01    0.38
    0.04   -0.06    0.20    0.36
   -0.51   -0.35   -0.46   -0.41    1.02
   -0.16    0.15    0.20    0.16   -0.74    0.48
    0.03   -0.02    0.19    0.32   -0.64    0.25    0.36
    0.19    0.20   -0.11    0.15   -0.18   -0.14    0.13    0.43
   -0.21    0.11    0.21    0.18   -0.29    0.37    0.13   -0.19    0.54
   -0.45   -0.82   -0.83   -0.78   -0.13   -0.95   -0.86   -0.58   -0.69    0.75
   -0.45   -0.74   -0.90   -0.75   -0.02   -0.74   -0.80   -0.56   -0.50    0.48    0.61
   -0.20    0.04    0.38    0.16   -0.81    0.30    0.25   -0.16    0.14   -1.01   -1.06    0.49
   -0.47   -0.83   -0.97   -0.90   -0.29   -0.97   -0.87   -0.61   -0.86    0.67    0.50   -1.03    0.97
   -0.47   -0.79   -0.71   -0.62    0.39   -0.85   -0.81   -0.52   -0.43    0.45    0.48   -1.03    0.35    0.61
    0.17    0.14   -0.12   -0.15   -0.65    0.15   -0.13   -0.14    0.14   -0.78   -0.67   -0.14   -0.82   -0.76    0.56
    0.16    0.05   -0.02   -0.14   -0.20   -0.20   -0.19    0.00   -0.15   -0.68   -0.70   -0.14   -0.75   -0.53    0.24    0.48
    0.18    0.00    0.11   -0.10   -0.62   -0.07   -0.09   -0.09   -0.13   -0.59   -0.77    0.09   -0.61   -0.75    0.25    0.28    0.45
   -0.51   -0.26   -0.79   -0.64    0.82   -0.83   -0.66   -0.15   -0.70   -0.23    0.13   -0.92    0.04    0.25   -0.71   -0.29   -0.70    1.42
   -0.34   -0.31    0.12    0.09    0.40   -0.02   -0.11   -0.35    0.35   -0.35   -0.27   -0.12   -0.56    0.14   -0.20   -0.04   -0.27    0.00    0.84
   -0.06   -0.54   -0.69   -0.39   -0.19   -0.68   -0.42   -0.15   -0.59    0.41    0.41   -0.79    0.41    0.36   -0.47   -0.44   -0.44   -0.17   -0.39    0.54
//
H MIYT790101
D Amino acid pair distance (Miyata et al., 1979)
R PMID:439147
A Miyata, T., Miyazawa, S. and Yasunaga, T.
T Two types of amino acid substitutions in protein evolution
J J. Mol. Evol. 12, 219-236 (1979)
M rows = ARNDCQEGHILKMFPSTWYV, cols = ARNDCQEGHILKMFPSTWYV
      0.
    2.92      0.
    1.78    2.04      0.
    2.37    2.34    0.65      0.
    1.39    3.06    2.83    3.48      0.
    1.92    1.13    0.99    1.47    2.48      0.
    2.46    1.45    0.85    0.90    3.26    0.84      0.
    0.91    3.58    1.96    2.37    2.22    2.48    2.78      0.
    2.17    0.82    1.29    1.72    2.56    0.32    0.96    2.78      0.
    2.69    2.49    3.37    3.98    1.63    2.57    3.39    3.60    2.45      0.
    2.76    2.62    3.49    4.10    1.65    2.70    3.53    3.67    2.59    0.14      0.
    2.96    0.40    1.84    2.05    3.27    1.06    1.14    3.54    0.79    2.84    2.98      0.
    2.42    2.29    3.08    3.69    1.46    2.30    3.13    3.34    2.19    0.29    0.41    2.63      0.
    3.23    2.47    3.70    4.27    2.24    2.81    3.59    4.14    2.63    0.61    0.63    2.85    0.82      0.
    0.06    2.90    1.80    2.40    1.33    1.92    2.48    0.97    2.15    2.62    2.70    2.94    2.36    3.17      0.
    0.51    2.74    1.31    1.87    1.84    1.65    2.06    0.85    1.94    2.95    3.04    2.71    2.67    3.45    0.56      0.
    0.90    2.03    1.40    2.05    1.45    1.12    1.83    1.70    1.32    2.14    2.25    2.10    1.86    2.60    0.87    0.89      0.
    4.23    2.72    4.39    4.88    3.34    3.42    4.08    5.13    3.16    1.72    1.73    3.11    1.89    1.11    4.17    4.38    3.50      0.
    3.18    2.02    3.42    3.95    2.38    2.48    3.22    4.08    2.27    0.86    0.94    2.42    0.93    0.48    3.12    3.33    2.45    1.06      0.
    1.85    2.43    2.76    3.40    0.86    2.13    2.97    2.76    2.11    0.85    0.91    2.70    0.62    1.43    1.79    2.15    1.42    2.51    1.52      0.
//
H MOHR870101
D EMPAR matrix (Mohana Rao, 1987)
R PMID:3570667
A Mohana Rao, J.K.
T New scoring matrix for amino acid residue exchanges based on residue
  characteristic physical parameters
J Int. J. Peptide Protein Res. 29, 276-281 (1987)
M rows = ARNDCQEGHILKMFPSTWYV, cols = ARNDCQEGHILKMFPSTWYV
     16.
      8.     16.
      9.     10.     16.
      9.     10.     11.     16.
     11.      8.      9.      8.     16.
     11.     10.     11.     11.     10.     16.
     10.      9.     10.     11.      9.     11.     16.
      8.      7.     10.      9.      8.      8.      6.     16.
     11.     10.     10.      9.     10.     11.     11.      7.     16.
      9.      4.      5.      3.      8.      6.      4.      6.      8.     16.
     11.      6.      7.      6.     11.      9.      7.      6.     10.     10.     16.
     10.     11.     11.     11.      9.     12.     11.      7.     11.      4.      7.     16.
     11.      6.      6.      5.     10.      9.      8.      4.     10.      9.     11.      8.     16.
     10.      5.      6.      4.     10.      7.      6.      7.      9.     12.     11.      6.     10.     16.
      6.      6.      9.      8.      7.      7.      5.     11.      5.      3.      4.      6.      2.      4.     16.
     10.      9.     11.     10.     10.     10.      9.     11.     10.      8.      8.     10.      7.      8.     10.     16.
     10.      9.     10.      9.     10.     10.      8.     10.     10.     10.      9.      9.      8.     10.      8.     11.     16.
     11.      7.      8.      6.     11.      9.      7.      8.     10.     11.     11.      7.     10.     11.      6.     10.     11.     16.
      9.      7.      8.      7.     10.      8.      6.     10.      9.     10.      9.      7.      8.     10.      8.     11.     11.     11.     16.
      9.      5.      5.      3.      8.      6.      4.      6.      9.     12.     10.      5.      9.     11.      3.      8.     10.     11.     10.     16.
//
H NIEK910101
D Structure-derived correlation matrix 1 (Niefind-Schomburg, 1991)
R PMID:2051484
A Niefind, K. and Schomburg, D.
T Amino acid similarity coefficients for protein modeling and sequence
  alignment derived from main-chain folding angles
J J. Mol. Biol. 219, 481-497 (1991)
M rows = ARNDCQEGHILKMFPSTWYV, cols = ARNDCQEGHILKMFPSTWYV
    1.00
    0.09    1.00
   -0.29   -0.10    1.00
    0.05   -0.08    0.30    1.00
   -0.35   -0.17    0.04   -0.10    1.00
    0.32    0.05   -0.14    0.11   -0.16    1.00
    0.70    0.09   -0.24    0.07   -0.34    0.39    1.00
   -0.40   -0.18    0.37    0.08    0.12   -0.28   -0.45    1.00
   -0.18    0.15    0.04   -0.01   -0.04    0.08   -0.14    0.06    1.00
   -0.25    0.05   -0.06   -0.28   -0.15   -0.13   -0.14   -0.23    0.01    1.00
    0.51    0.00   -0.23    0.01   -0.27    0.29    0.57   -0.54   -0.09    0.25    1.00
    0.55    0.14   -0.19    0.13   -0.25    0.16    0.50   -0.34   -0.23   -0.17    0.31    1.00
    0.39   -0.10   -0.13   -0.09   -0.25    0.22    0.36   -0.29   -0.08    0.15    0.41    0.05    1.00
   -0.18    0.15   -0.13   -0.31   -0.05   -0.25   -0.24   -0.05    0.17    0.27   -0.08   -0.16   -0.02    1.00
    0.10   -0.18   -0.10    0.02    0.13   -0.18   -0.08    0.10   -0.32   -0.53   -0.25    0.04   -0.31   -0.28    1.00
   -0.38   -0.10    0.04    0.02    0.31   -0.23   -0.41    0.28   -0.05   -0.34   -0.61   -0.18   -0.48   -0.13    0.35    1.00
   -0.59   -0.12    0.01   -0.18    0.12   -0.21   -0.50    0.10    0.10    0.30   -0.31   -0.33   -0.31    0.19   -0.21    0.33    1.00
   -0.11    0.00   -0.21   -0.19    0.00   -0.17   -0.12   -0.10   -0.01    0.03   -0.12    0.02   -0.19    0.15   -0.03    0.05    0.07    1.00
   -0.59   -0.01    0.04   -0.19    0.25   -0.28   -0.57    0.19    0.13    0.13   -0.46   -0.43   -0.31    0.24   -0.13    0.34    0.46    0.06    1.00
   -0.23   -0.03   -0.15   -0.22   -0.10   -0.03   -0.09   -0.24   -0.11    0.67    0.23   -0.13    0.08    0.13   -0.42   -0.25    0.35   -0.04    0.15    1.00
//
H NIEK910102
D Structure-derived correlation matrix 2 (Niefind-Schomburg, 1991)
R PMID:2051484
A Niefind, K. and Schomburg, D.
T Amino acid similarity coefficients for protein modeling and sequence
  alignment derived from main-chain folding angles
J J. Mol. Biol. 219, 481-497 (1991)
M rows = ARNDCQEGHILKMFPSTWYV, cols = ARNDCQEGHILKMFPSTWYV
    1.00
    0.11    1.00
   -0.31   -0.12    1.00
    0.07   -0.08    0.35    1.00
   -0.38   -0.20    0.04   -0.10    1.00
    0.36    0.10   -0.16    0.13   -0.16    1.00
    0.74    0.11   -0.27    0.09   -0.36    0.42    1.00
   -0.41   -0.21    0.40    0.08    0.13   -0.32   -0.46    1.00
   -0.20    0.19    0.04    0.00   -0.01    0.12   -0.14    0.09    1.00
   -0.26    0.06   -0.07   -0.29   -0.16   -0.15   -0.13   -0.24    0.00    1.00
    0.54    0.03   -0.24    0.01   -0.29    0.35    0.62   -0.56   -0.13    0.27    1.00
    0.60    0.21   -0.22    0.14   -0.31    0.23    0.58   -0.38   -0.26   -0.18    0.36    1.00
    0.43   -0.09   -0.13   -0.08   -0.29    0.22    0.38   -0.30   -0.06    0.18    0.47    0.09    1.00
   -0.19    0.20   -0.12   -0.35   -0.07   -0.26   -0.27   -0.05    0.20    0.32   -0.08   -0.18   -0.01    1.00
    0.11   -0.21   -0.10    0.01    0.14   -0.18    0.07    0.09   -0.34   -0.55   -0.26    0.04   -0.32   -0.31    1.00
   -0.40   -0.13    0.06    0.03    0.35   -0.22   -0.43    0.28   -0.02   -0.37   -0.66   -0.21   -0.53   -0.13    0.35    1.00
   -0.63   -0.12    0.01   -0.19    0.15   -0.22   -0.54    0.11    0.09    0.32   -0.36   -0.38   -0.35    0.21   -0.21    0.36    1.00
   -0.11    0.03   -0.24   -0.22   -0.02   -0.18   -0.12   -0.11   -0.02    0.04   -0.15    0.02   -0.19    0.18   -0.02    0.07    0.12    1.00
   -0.63   -0.01    0.05   -0.22    0.29   -0.32   -0.62    0.20    0.14    0.15   -0.48   -0.48   -0.33    0.29   -0.15    0.36    0.52    0.11    1.00
   -0.25   -0.04   -0.16   -0.25   -0.10   -0.04   -0.09   -0.25   -0.13    0.72    0.25   -0.16    0.11    0.16   -0.44   -0.27    0.38   -0.02    0.17    1.00
//
H OVEJ920101
D STR matrix from structure-based alignments (Overington et al., 1992)
R PMID:1304904
A Overington, J., Donnelly, D., Johnson, M.S., Sali, A. and Blundell, T.L.
T Environment-specific amino acid substitution tables: tertiary templates
  and prediction of protein folds
J Protein Science 1, 216-226 (1992)
M rows = ARNDCQEGHILKMFPSTWYV, cols = ARNDCQEGHILKMFPSTWYV
      4.
     -1.      7.
     -1.     -1.      5.
     -1.     -2.      2.      6.
     -2.     -2.     -6.     -7.     11.
      0.      1.      0.      0.     -3.      6.
      0.      0.      0.      2.     -3.      2.      5.
      0.     -2.     -1.     -1.     -6.     -2.     -2.      5.
     -2.      0.      2.      0.     -6.      0.     -2.     -3.      8.
     -2.     -3.     -3.     -3.     -4.     -5.     -3.     -5.     -5.      6.
     -2.     -3.     -3.     -6.     -6.     -3.     -4.     -5.     -3.      2.      5.
     -1.      2.      0.     -1.     -4.      1.      1.     -3.      0.     -3.     -2.      5.
      0.     -4.     -2.     -4.     -5.      1.     -2.     -4.     -2.      1.      3.     -1.      8.
     -3.     -4.     -3.     -5.     -2.     -4.     -4.     -6.     -2.      1.      2.     -3.      0.      7.
     -1.     -2.     -2.     -1.     -8.     -2.     -1.     -2.     -3.     -4.     -3.     -1.     -6.     -5.      7.
      0.      0.      0.      0.     -4.     -1.     -1.     -1.     -2.     -3.     -4.     -1.     -4.     -3.     -1.      4.
     -1.     -1.      0.     -1.     -5.      0.      0.     -3.     -2.     -2.     -3.      0.     -2.     -3.     -1.      1.      5.
     -3.     -2.     -5.     -6.     -6.     -5.     -6.     -4.     -3.     -2.     -1.     -3.     -2.      2.     -4.     -5.     -5.     10.
     -3.     -1.     -1.     -3.     -6.     -3.     -2.     -3.      0.     -1.     -2.     -2.     -1.      3.     -6.     -2.     -2.      2.      7.
      0.     -3.     -4.     -4.     -4.     -2.     -2.     -4.     -2.      2.      1.     -3.      0.     -1.     -4.     -3.     -1.     -4.     -1.      5.
//
H QU_C930101
D Cross-correlation coefficients of preference factors
  main chain (Qu et al., 1993)
R PMID:8381879
A Qu, C., Lai, L., Xu, X. and Tang, Y.
T Phyletic relationships of protein structures based on spatial prefernce
  of residues
J J. Mol. Evol. 36, 67-78 (1993)
M rows = ARNDCQEGHILKMFPSTWYV, cols = ARNDCQEGHILKMFPSTWYV
   1.000
   0.390   1.000
   0.370   0.266   1.000
   0.299  -0.109   0.037   1.000
   0.270   0.273   0.105   0.035   1.000
   0.261  -0.084   0.082   0.321   0.191   1.000
   0.300   0.375   0.206   0.137   0.341   0.228   1.000
   0.407   0.394   0.293   0.250   0.246   0.494   0.164   1.000
   0.356   0.093   0.299  -0.117   0.527   0.630   0.121   0.497   1.000
   0.476   0.305   0.452   0.242  -0.029   0.372   0.212   0.429   0.406   1.000
   0.555   0.446   0.191   0.261   0.501   0.251   0.291   0.327   0.457   0.570   1.000
   0.398   0.236   0.208   0.184   0.054   0.323   0.247   0.006   0.072   0.088  -0.080   1.000
   0.207   0.374   0.438  -0.295  -0.006   0.211   0.128   0.326   0.461   0.440   0.112   0.285   1.000
   0.628   0.552   0.278   0.475   0.550   0.364   0.433   0.455   0.405   0.532   0.769   0.217   0.111   1.000
   0.183  -0.037   0.156   0.008   0.355  -0.168  -0.216  -0.023   0.304   0.065   0.079   0.099   0.266   0.091   1.000
   0.193  -0.043  -0.051   0.012  -0.178   0.404  -0.081   0.015   0.144   0.166  -0.042   0.102   0.165  -0.012  -0.363   1.000
  -0.083   0.037   0.076   0.328   0.087   0.344   0.220   0.335   0.259   0.385   0.386  -0.206  -0.141   0.306  -0.336  -0.124   1.000
   0.081  -0.059   0.277   0.578   0.174   0.515   0.149   0.136   0.232   0.357   0.268   0.436  -0.075   0.451  -0.118  -0.023   0.564   1.000
   0.683   0.201   0.387   0.320   0.195   0.207   0.273   0.372   0.083   0.333   0.246   0.436  -0.057   0.428  -0.054  -0.093   0.000   0.293   1.000
   0.565   0.531   0.512   0.149   0.427   0.334   0.444   0.639   0.534   0.641   0.598   0.249   0.278   0.626   0.020  -0.103   0.329   0.378   0.614   1.000
//
H QU_C930102
D Cross-correlation coefficients of preference factors
  side chain (Qu et al., 1993)
R PMID:8381879
A Qu, C., Lai, L., Xu, X. and Tang, Y.
T Phyletic relationships of protein structures based on spatial prefernce
  of residues
J J. Mol. Evol. 36, 67-78 (1993)
M rows = ARNDCQEGHILKMFPSTWYV, cols = ARNDCQEGHILKMFPSTWYV
   1.000
   0.250   1.000
   0.138   0.558   1.000
  -0.018  -0.054   0.452   1.000
   0.799   0.113   0.032   0.015   1.000
   0.550   0.243   0.222   0.257   0.418   1.000
  -0.116   0.037   0.408   0.851  -0.167   0.254   1.000
   0.000   0.000   0.000   0.000   0.000   0.000   0.000   0.000
   0.523   0.392   0.305   0.067   0.425   0.614  -0.102   0.000   1.000
   0.888   0.108  -0.101  -0.185   0.717   0.511  -0.135   0.000   0.378   1.000
   0.862   0.049  -0.172  -0.249   0.787   0.439  -0.223   0.000   0.289   0.960   1.000
   0.281   0.872   0.490  -0.064   0.002   0.377  -0.051   0.000   0.488   0.099  -0.004   1.000
   0.858   0.058  -0.090  -0.109   0.912   0.450  -0.180   0.000   0.441   0.842   0.881  -0.044   1.000
   0.874   0.108  -0.072  -0.107   0.857   0.482  -0.187   0.000   0.511   0.893   0.927   0.061   0.903   1.000
   0.656   0.133   0.265   0.276   0.558   0.598   0.097   0.000   0.651   0.572   0.504   0.206   0.523   0.661   1.000
   0.281   0.804   0.661   0.245   0.104   0.357   0.204   0.000   0.568   0.083   0.003   0.745   0.054   0.152   0.200   1.000
   0.574   0.427   0.519   0.382   0.326   0.610   0.287   0.000   0.399   0.382   0.346   0.540   0.313   0.410   0.435   0.601   1.000
   0.825   0.169   0.003  -0.079   0.779   0.478  -0.216   0.000   0.460   0.792   0.843   0.111   0.785   0.907   0.597   0.204   0.471   1.000
   0.772   0.266   0.338   0.225   0.817   0.550   0.036   0.000   0.492   0.573   0.625   0.182   0.764   0.743   0.632   0.307   0.540   0.802   1.000
   0.850   0.045  -0.203  -0.196   0.755   0.458  -0.186   0.000   0.284   0.946   0.973   0.024   0.874   0.909   0.462   0.005   0.396   0.835   0.632   1.000
//
H QU_C930103
D The mutant distance based on spatial preference factor (Qu et al., 1993)
R PMID:8381879
A Qu, C., Lai, L., Xu, X. and Tang, Y.
T Phyletic relationships of protein structures based on spatial prefernce
  of residues
J J. Mol. Evol. 36, 67-78 (1993)
M rows = ARNDCQEGHILKMFPSTWYV, cols = ARNDCQEGHILKMFPSTWYV
      8.
      2.      8.
      1.      2.      8.
      0.     -1.      3.      8.
      5.      0.      0.      0.      8.
      2.      0.      1.      2.      3.      8.
      0.      0.      3.      4.      0.      2.      8.
      2.      2.      2.      0.      1.      2.     -1.      8.
      4.      2.      2.      0.      4.      4.      0.      0.      8.
      5.      0.      0.      0.      4.      2.      0.      0.      3.      8.
      5.      0.      0.      0.      5.      3.      0.      1.      2.      6.      8.
      2.      6.      2.      0.      0.      1.      1.     -1.      3.      1.      0.      8.
      5.      0.      0.      0.      5.      2.      0.      2.      3.      5.      6.      0.      8.
      5.      0.      1.      0.      6.      3.      0.      0.      4.      5.      6.      1.      5.      8.
      3.      1.      3.      1.      4.      2.      0.      0.      4.      3.      2.      1.      3.      3.      8.
      2.      3.      3.      2.      1.      2.      2.      1.      3.      0.      0.      3.      0.      0.      1.      8.
      3.      2.      3.      4.      1.      3.      3.      1.      2.      1.      1.      3.      1.      2.      2.      4.      8.
      4.      0.      0.      0.      5.      2.      0.     -1.      3.      4.      4.      1.      4.      6.      3.      1.      2.      8.
      4.      0.      2.      1.      4.      2.      1.      0.      3.      4.      4.      1.      4.      4.      3.      2.      3.      5.      8.
      5.      0.      0.      0.      5.      3.      0.      2.      2.      6.      6.      0.      6.      5.      2.      0.      2.      5.      5.      8.
//
H RISJ880101
D Scoring matrix (Risler et al., 1988)
R PMID:3221397
A Risler, J.L., Delorme, M.O., Delacroix, H. and Henaut, A.
T Amino acid substitutions in structurally related proteins
  A pattern recognition approach
  Determination of a new and efficient scoring matrix
J J. Mol. Biol. 204, 1019-1029 (1988)
M rows = ARNDCQEGHILKMFPSTWYV, cols = ARNDCQEGHILKMFPSTWYV
     2.2
     1.5     2.2
     1.3     1.2     2.2
     0.2    -0.1     0.8     2.2
    -1.5    -1.5    -1.6    -1.7     2.2
     1.8     2.0     1.6     0.6    -1.4     2.2
     1.7     1.9     1.4     1.0    -1.5     2.1     2.2
     0.6     0.1     0.2    -0.4    -1.7     0.2     0.3     2.2
    -0.6    -0.4    -0.3    -1.3    -1.8    -0.5    -0.6    -1.2     2.2
     1.7     1.4     0.9     0.0    -1.6     1.4     1.5     0.0    -0.8     2.2
     1.3     1.2     0.8    -0.2    -1.5     1.1     0.9    -0.2    -0.9     2.1     2.2
     1.4     2.1     1.0     0.1    -1.6     1.7     1.4    -0.1    -1.0     1.0     0.7     2.2
     1.0     1.1     0.0    -0.5    -1.6     1.2     0.6    -0.4    -1.2     0.9     1.8     0.4     2.2
     0.6     0.4     0.4    -0.3    -1.6     0.7     0.6    -0.4    -1.1     1.0     1.0     0.1    -0.2     2.2
    -0.2    -0.3    -1.0    -1.2    -1.8    -0.6    -0.1    -1.2    -1.6    -0.6    -0.8    -0.7    -1.2    -1.1     2.2
     2.0     2.0     1.9     0.7    -1.3     1.8     1.8     0.7    -0.4     1.6     1.3     1.4     0.6     0.5    -0.3     2.2
     1.9     1.9     1.1     0.0    -1.4     1.7     1.6     0.2    -0.9     1.6     1.2     1.2     0.8     0.3    -0.5     2.1     2.2
    -0.9    -0.8    -1.1    -1.4    -1.8    -1.0    -1.0    -1.3    -1.7    -0.7    -0.8    -1.1    -1.3    -0.9    -1.6    -0.8    -1.0     2.2
     0.2     0.8    -0.1    -0.4    -1.1     0.5     0.2    -0.2    -0.8     0.4     0.5     0.5    -0.2     2.0    -1.2     0.4     0.3    -0.6     2.2
     2.0     1.5     1.1     0.0    -1.4     1.5     1.6     0.1    -0.7     2.2     2.0     1.2     0.8     0.8    -0.6     1.8     1.6    -0.7     0.3     2.2
//
H TUDE900101
D isomorphicity of replacements (Tudos et al., 1990)
R PMID:2279846
A Tudos, E., Cserzo, M. and Simon, I.
T Predicting isomorphic residue replacements for protein design
J Int. J. Peptide Protein Res. 36, 236-239 (1990)
* Diagonal elements are missing.
* We use 100 as diagonal elements.
M rows = ARNDCQEGHILKMFPSTWYV, cols = ARNDCQEGHILKMFPSTWYV
    100.
     -2.    100.
     -8.     11.    100.
      3.      2.     32.    100.
      4.    -12.     -7.    -20.    100.
      0.     26.     12.      8.     -8.    100.
     12.     11.     13.     34.    -18.     37.    100.
     -3.     -6.     10.      8.     -1.    -10.     -5.    100.
    -10.      0.      8.     10.      3.     -4.     -8.     -8.    100.
    -17.    -25.    -32.    -39.     12.    -20.    -36.    -21.      3.    100.
     -6.    -24.    -35.    -40.     15.    -26.    -40.    -16.     -9.     46.    100.
      2.     24.     17.     10.    -14.     26.     24.    -11.     -4.    -17.    -33.    100.
     -2.      0.    -12.    -16.      2.    -12.    -17.    -10.     -8.     18.     24.    -19.    100.
     -8.    -11.    -23.    -31.     11.    -22.    -40.    -12.    -10.     32.     36.    -26.     20.    100.
     -2.     -4.      8.      1.     -3.      0.     -7.      4.     -2.    -18.    -16.     -2.    -10.     -2.    100.
     10.    -10.      1.      7.     -6.     -7.    -10.      9.     -3.    -17.    -11.    -10.    -10.      0.     15.    100.
     -3.     -5.     12.     11.     -4.    -10.    -12.    -13.     -7.     -5.    -11.     -8.     -8.      4.      2.     24.    100.
    -12.     -7.     -6.    -20.      8.     -3.    -10.    -13.     -6.     12.      8.    -10.     12.      8.     -9.    -18.     -8.    100.
    -18.      0.    -13.    -22.      5.    -23.    -28.    -18.     12.     29.     16.    -21.      8.     24.     -9.    -16.     -2.      6.    100.
    -12.    -18.    -30.    -32.      8.    -12.    -20.    -14.    -10.     46.     26.    -14.     10.     16.    -18.    -16.     -4.     14.     17.    100.
//
H AZAE970101
D The single residue substitution matrix from interchanges of
  spatially neighbouring residues (Azarya-Sprinzak et al., 1997)
R PMID:9488136
A Azarya-Sprinzak, E., Naor, D., Wolfson, H.J. and Nussinov, R.
T Interchanges of spatially neighbouring residues in structurally conserved
  environments.
J Protein Engineering 10, 1109-1122 (1997)
M rows = ARNDCQEGHILKMFPSTWYV, cols = ARNDCQEGHILKMFPSTWYV
      14
       1      16
       1      10      15
       0      13      16      26
       5      -9      -4      -8      18
       0      16      13      16     -10      21
       2      13      10      15      -8      17      11
       5       0       8       7       1       0       1      24
      -2       4       5       8      -2       6       4       6       7
      -6     -11     -11     -14       2     -12     -11     -10      -4      10
      -2      -8      -9     -11       1      -9      -8      -9      -5       8       9
       1      21      12      16     -11      22      17      -1       3     -13     -10      28
       2      -1      -3      -7       0      -2       1      -3      -1       2       5      -4       2
      -4      -8      -9     -10       2     -10      -7      -4      -1       6       5     -11       2       8
       2       2      11      11       0       1       5      13       4     -14     -12       5     -10      -6      51
       1       6       7       8      -1       6       6       8       3      -8      -7       6      -5      -5       6       9
      -2       5       4       4      -5       6       3       1       4      -4      -6       7      -4      -4       5       5      10
      -2      -3      -5      -5      -1      -3      -6      -1       3       4       2      -8       2       5      -5      -4      -2       8
      -2      -1      -3      -4      -1      -3      -1      -2       0       2       0      -3       1       3      -5      -1       0       2       4
      -5     -11     -11     -13       3     -12     -12      -8      -4       9       5     -14       0       5      -7      -6      -3       4       2      11
//
H AZAE970102
D The substitution matrix derived from spatially conserved motifs
  (Azarya-Sprinzak et al., 1997)
R PMID:9488136
A Azarya-Sprinzak, E., Naor, D., Wolfson, H.J. and Nussinov, R.
T Interchanges of spatially neighbouring residues in structurally conserved
  environments.
J Protein Engineering 10, 1109-1122 (1997)
M rows = ARNDCQEGHILKMFPSTWYV, cols = ARNDCQEGHILKMFPSTWYV
       8
       1      11
       0       7      11
       0       9      12      16
       2      -7      -5      -8      14
       1      12      10      13      -9      17
       1      10       8      10      -6      13       8
       1       0       7       8       0       0       0      18
      -2       2       2       4      -1       2       1       5       5
      -3     -10     -11     -12       4     -12     -10      -8      -3      11
       0      -7      -9     -10       2      -9      -7      -8      -4       8      10
       1      14      10      11     -10      16      13       0       2     -12      -9      20
       1      -2      -4      -6       1      -3       0      -5      -2       3       6      -5       4
      -2      -8      -9      -9       3     -10      -7      -3      -1       7       6     -10       3       8
      -1       1       8       7      -2       0       0      10       3      -9      -9       1      -9      -5      33
       0       4       6       6      -2       4       3       6       2      -7      -6       4      -5      -5       5       7
      -2       2       2       3      -3       2       1       1       3      -2      -4       2      -3      -3       3       4       6
      -1      -4      -4      -4       0      -5      -5      -1      -1       4       3      -7       2       4      -4      -3      -1       6
      -1      -3      -4      -5       0      -4      -1      -1       0       3       2      -4       2       3      -4      -1       0       2       3
      -4     -10     -11     -12       5     -12     -11      -7      -3      11       6     -13       1       7      -5      -5      -1       4       2      12
//
H RIER950101
D Hydrophobicity scoring matrix (Riek et al., 1995)
R PMID:7715195
A Riek, R.P., Handschumacher, M.D., Sung, S.S., Tan, M., Glynias, M.J.,
  Schluchter, M.D., Novotny, J. and Graham, R.M.
T Evolutionary conservation of both the hydrophilic and hydrophobic nature of
  transmembrane residues.
J J. Theor. Biol. 172, 245-258 (1995)
M rows = ARNDCQEGHILKMFPSTWYV, cols = ARNDCQEGHILKMFPSTWYV
     100
      13     100
      60      53     100
      33      81      73     100
      98      11      58      30     100
      64      49      96      68      62     100
      39      74      79      94      36      74     100
      96      17      64      36      94      68      43     100
      71      42      89      61      69      93      68      75     100
      91       4      51      23      93      55      29      87      62     100
      93       6      52      25      95      57      31      89      64      98     100
      35      78      75      98      33      71      96      39      64      26      27     100
      89       2      49      21      91      53      27      85      60      98      96      24     100
      87       0      47      19      89      51      26      83      58      96      94      22      98     100
      89      24      71      44      86      76      50      93      83      79      81      46      78      76     100
      94      19      66      39      91      71      45      98      78      84      86      41      83      81      95     100
      98      16      63      35      95      67      41      99      74      88      90      38      86      84      91      96     100
      98      11      58      31      99      63      37      94      69      93      94      33      91      89      87      92      96     100
      94      19      66      38      92      70      44      98      77      85      87      41      83      81      94      99      97      93     100
      94       7      54      26      96      58      33      90      65      97      99      29      95      93      83      88      91      96      88     100
//
H WEIL970101
D WAC matrix constructed from amino acid comparative profiles (Wei et al., 1997)
R PMID:9390315
A Wei, L., Altman, R.B. and Chang, J.T.
T Using the radial distributions of physical features to compare amino
  acid environments and align amino acid sequences.
J Pac. Symp. Biocomput. 1997 5, 465-476 (1997)
M rows = ARNDCQEGHILKMFPSTWYV, cols = ARNDCQEGHILKMFPSTWYV
       4
      -1       4
       0       0       4
      -2      -1       0       4
       0      -1       0      -2       4
       0       0       1      -1       0       4
      -3      -1       0       0      -2       0       4
      -1      -1       0      -2       0       0      -2       4
       0       0       0      -1       0       0      -1      -1       4
       0      -2      -1      -4       0       0      -4      -2      -1       4
       0      -1      -1      -3       0       0      -3      -1      -1       1       4
      -1       2       0      -1      -2       0      -1      -1       0      -2      -2       4
       1       0       0      -1       1       1      -1       0       0       2       2       0       4
       0      -2      -1      -4       0       0      -4      -2       0       0       1      -2       2       4
       0       0       0      -1      -1       0      -1       0       0       0       0       0       1       0       4
       0      -1       1      -1       0       0      -2       0      -1      -1      -1       0       0      -2       0       4
       0       0       1      -1       0       1      -1       0      -1       0       0       0       0      -2       0       1       4
       0       0      -1      -3       0       0      -2      -2       0       0       1      -2       2       2       0      -1      -1       4
       0      -1       0      -3       0       1      -4      -2       0       0       0      -2       0       1      -1      -1      -1       1       4
       1      -2      -1      -3       0      -1      -4      -2      -1       2       1      -3       1       0       0      -1       0       0       0       4
//
H WEIL970102
D Difference matrix obtained by subtracting the BLOSUM62 from the WAC
  matrix (Wei et al., 1997)
R PMID:9390315
A Wei, L., Altman, R.B. and Chang, J.T.
T Using the radial distributions of physical features to compare amino
  acid environments and align amino acid sequences.
J Pac. Symp. Biocomput. 1997 5, 465-476 (1997)
M rows = ARNDCQEGHILKMFPSTWYV, cols = ARNDCQEGHILKMFPSTWYV
       0
       0      -1
       2       0      -2
       0       1      -1      -2
       0       2       3       1      -5
       1      -1       1      -1       3      -1
      -2      -1       0      -2       2      -2      -1
      -1       1       0      -1       3       2       0      -2
       2       0      -1       0       3       0      -1       1      -4
       1       1       2      -1       1       3      -1       2       2       0
       1       1       2       1       1       2       0       3       2      -1       0
       0       0       0       0       1      -1      -2       1       1       1       0      -1
       2       1       2       2       2       1       1       3       2       1       0       1      -1
       2       1       2      -1       2       3      -1       1       1       0       1       1       2      -2
       1       2       2       0       2       1       0       2       2       3       3       1       3       4      -3
      -1       0       0      -1       1       0      -2       0       0       1       1       0       1       0       1       0
       0       1       1       0       1       2       0       2       1       1       1       1       1       0       1       0      -1
       3       3       3       1       2       2       1       0       2       3       3       1       3      -1       4       2       1      -7
       2       1       2       0       2       2      -2       1      -2       1       1       0       1       0       2       1       1      -1      -3
       1       1       2       0       1       1      -2       1       2      -1       0      -1       0       1       2       1       0       3       1       0
//
H MEHP950101
D (Mehta et al., 1995)
R PMID:8580842
A Mehta, P.K., Heringa, J. and Argos, P.
T A simple and fast approach to prediction of protein secondary structure from
  multiply aligned sequences with accuracy above 70%
J Protein Science 4, 2517-2525 (1995)
M rows = ARNDCQEGHILKMFPSTWYV, cols = ARNDCQEGHILKMFPSTWYV
    1.23
    1.17    1.06
    1.28    1.03    1.02
    1.31    1.18    1.08    1.11
    1.41    1.21    1.36    1.44    1.04
    1.31    1.10    1.20    1.25    1.49    1.16
    1.34    1.15    1.21    1.31    1.43    1.26    1.19
    1.11    0.99    0.96    1.02    1.36    1.11    1.06    0.86
    1.17    1.06    1.13    1.05    1.50    1.22    1.23    1.10    0.99
    1.08    0.91    0.89    0.93    1.24    1.02    0.96    0.79    0.86    0.90
    1.19    1.02    0.98    1.00    1.41    1.01    1.01    0.88    1.08    0.99    1.04
    1.29    1.11    1.14    1.18    1.31    1.21    1.22    1.05    1.10    0.94    1.07    1.13
    1.20    0.97    1.01    0.94    1.36    1.10    1.02    0.81    1.08    1.01    1.08    0.99    1.04
    0.94    0.74    0.83    0.79    1.16    0.88    0.91    0.68    0.94    0.74    0.90    0.78    0.91    0.82
    0.94    0.69    0.74    0.84    1.30    0.91    0.96    0.92    0.80    0.67    0.75    0.67    0.59    0.69    0.75
    1.17    0.90    1.01    0.97    1.33    1.09    1.02    0.94    1.03    0.89    1.01    0.98    0.59    0.78    0.79    0.93
    1.06    0.88    0.93    1.01    1.18    1.02    0.94    0.86    0.95       -    0.90    0.88    0.96    0.72    0.80    0.87    0.85
    0.90    0.63    0.88    0.87    0.78    0.95    0.86    0.58    0.92    0.53    0.72    0.74    0.75    0.66    0.40    0.69    0.74    0.91
    0.86    0.75    0.83    0.73    1.00    0.85    0.76    0.58    0.81    0.68    0.79    0.79    0.86    0.71    0.54    0.63    0.65    0.66    0.80
    1.09    0.98    0.96    1.01    1.33    1.06    1.04    0.95    1.01    0.83    0.88    0.99    1.02    0.76    0.77    0.93    0.84    0.60    0.67    0.83
//
H MEHP950102
D (Mehta et al., 1995)
R PMID:8580842
A Mehta, P.K., Heringa, J. and Argos, P.
T A simple and fast approach to prediction of protein secondary structure from
  multiply aligned sequences with accuracy above 70%
J Protein Science 4, 2517-2525 (1995)
M rows = ARNDCQEGHILKMFPSTWYV, cols = ARNDCQEGHILKMFPSTWYV
    0.75
    0.80    0.90
    0.71    0.88    0.80
    0.56    0.63    0.69    0.66
    0.75    0.84    0.72    0.67    1.07
    0.68    0.83    0.71    0.64    0.65    0.80
    0.63    0.82    0.74    0.58    0.69    0.73    0.74
    0.83    0.84    0.71    0.61    0.80    0.78    0.87    0.97
    0.79    0.92    0.78    0.68    0.69    0.79    0.78    0.71    0.99
    1.11    1.23    1.12    1.06    0.96    1.10    1.15    1.25    1.24    1.33
    0.97    1.05    0.97    0.96    0.84    1.07    1.12    1.09    1.07    1.21    1.12
    0.65    0.84    0.72    0.64    0.79    0.75    0.78    0.76    0.82    1.11    0.99    0.78
    0.97    1.14    0.92    0.93    0.97    0.97    0.96    1.18    0.96    1.16    1.06    1.03    1.05
    1.16    1.26    1.11    1.17    1.04    1.07    1.17    1.30    1.05    1.54    1.27    1.11    1.21    1.33
    0.77    1.03    0.91    0.75    0.67    0.83    0.75    0.75    0.83    1.30    1.21    0.92    1.34    1.07    0.82
    0.80    0.99    0.84    0.77    0.81    0.85    0.92    0.91    0.85    1.24    1.09    0.89    1.15    1.28    0.87    0.96
    0.97    1.08    0.99    0.88    0.93    1.02    1.11    1.03    0.91    1.27    1.18    1.09    1.11    1.32    0.93    1.10    1.16
    1.18    1.33    0.95    1.04    1.47    1.17    1.33    1.28    1.18    1.71    1.37    1.11    1.35    1.31    1.09    1.34    1.42    1.22
    1.23    1.25    1.08    1.12    1.22    1.11    1.31    1.27    1.23    1.51    1.41    1.18    1.23    1.34    1.29    1.41    1.46    1.29    1.31
    1.05    1.08    1.05    0.99    0.91    1.03    1.08    1.09    1.13    1.42    1.35    1.06    1.22    1.51    1.13    1.21    1.27    1.63    1.60    1.41
//
H MEHP950103
D (Mehta et al., 1995)
R PMID:8580842
A Mehta, P.K., Heringa, J. and Argos, P.
T A simple and fast approach to prediction of protein secondary structure from
  multiply aligned sequences with accuracy above 70%
J Protein Science 4, 2517-2525 (1995)
M rows = ARNDCQEGHILKMFPSTWYV, cols = ARNDCQEGHILKMFPSTWYV
    0.86
    1.02    1.06
    0.95    1.19    1.36
    1.23    1.41    1.52    1.43
    0.49    0.82    0.70    0.60    0.71
    0.92    1.13    1.13    1.17    0.51    0.96
    0.96    1.02    1.04    1.17    0.57    0.96    1.01
    1.11    1.41    1.80    1.88    0.51    1.22    1.15    1.50
    1.04    1.02    1.18    1.63    0.39    0.92    0.91    1.40    1.05
    0.51    0.69    1.00    1.04    0.43    0.70    0.74    0.98    0.81    0.58
    0.57    0.82    1.13    1.09    0.28    0.80    0.69    1.10    0.62       -    0.61
    1.06    1.08    1.30    1.38    0.68    1.02    0.93    1.43    1.15    0.91    0.84    1.10
    0.53    0.74    1.17    1.34    0.10    0.79    1.02    1.07    0.88    0.59    0.63    0.97    0.77
    0.79    1.09    1.19    1.17    0.46    1.16    0.85    1.16    1.05    0.42    0.63    1.33    0.74    0.83
    1.69    1.76    1.91    2.04    0.96    1.63    1.71    1.80    1.96    1.18    1.19    2.08    1.28    1.66    2.13
    1.04    1.29    1.35    1.63    0.55    1.12    1.13    1.37    1.29    0.74    0.74    1.32    0.79    0.94    1.87    1.29
    0.92    1.13    1.23    1.27    0.68    0.89    0.89    1.30    1.33    0.79    0.84    1.12    0.83    0.97    1.71    1.11    1.08
    0.86    1.22    1.46    1.24    0.47    0.73    0.61    1.46    0.78    0.56    0.88    1.44    0.83    1.19    2.39    1.01    0.69    0.78
    0.84    1.10    1.27    1.46    0.48    1.14    0.91    1.51    0.97    0.65    0.57    1.13    0.84    0.99    1.54    1.03    0.85    1.22    0.83
    0.65    0.86    0.99    0.99    0.32    0.77    0.71    0.90    0.66    0.45    0.49    0.89    0.44    0.44    1.32    0.70    0.78    0.57    0.48    0.63
//
H KAPO950101
D (Kapp et al., 1995)
R PMID:8535255
A Kapp, O.H., Moens, L., Vanfleteren, J., Trotman, C.N., Suzuki, T. and
  Vinogradov, S.N.
T Alignment of 700 globin sequences: extent of amino acid substitution and its
  correlation with variation in volume
J Protein Science 4, 2179-2190 (1995)
M rows = ARNDCQEGHILKMFPSTWYV, cols = ARNDCQEGHILKMFPSTWYV
   23.40
   16.80   29.50
   17.10   17.10   27.40
   18.20   18.20   21.40   25.90
   21.50   14.40   14.70   14.00   31.90
   17.20   19.60   18.60   22.20   13.80   96.50
   18.10   18.70   20.00   22.80   12.20   20.40   26.50
   19.90   16.10   18.10   18.70   15.00   16.30   19.30   26.80
   11.50   13.70   18.90   17.20   13.50   21.20   15.70   12.20   30.80
   17.20   14.30   14.80   13.70   20.90   15.80   14.90   14.70   12.40   24.70
   13.60   12.20   11.70   12.50   15.50   13.30   11.40   11.50    9.07   21.00   24.80
   17.10   21.90   17.70   18.20    9.83   22.00   19.20   15.60   15.50   14.20   12.10   26.40
   16.20   15.50   13.70   15.50   19.80   17.80   15.20   15.00   11.40   20.90   22.40   15.40   25.90
   11.90   10.10   11.40    9.04   13.50   11.50    9.24    9.84   10.70   18.40   20.60    9.68   20.20   27.10
   17.70   15.70   14.60   19.40    5.43   18.00   19.10   17.00   11.70    9.35    7.28   16.80   11.60    3.14   32.20
   20.40   17.50   20.90   19.10   17.70   17.60   17.70   20.20   13.80   14.60   12.20   16.60   14.70    9.65   17.90   25.40
   18.10   20.60   20.20   19.00   16.20   17.40   18.80   18.20   14.80   17.50   14.30   17.60   16.90   12.80   14.90   19.50   26.10
   10.10    9.94    7.74    9.08    9.56   16.60   15.30    7.20    0.00   10.40   14.70    7.79   18.50   19.30    9.85    9.70   17.20   33.80
   15.30   13.80   20.10   14.90   17.30   14.60   12.70   13.70   19.40   17.60   17.90   14.70   20.00   22.60    6.99   14.40   17.70   19.50   29.20
   16.70   14.40   14.80   15.10   21.40   15.20   15.10   14.50   12.90   22.20   18.90   13.50   19.10   17.20   11.10   15.10   17.90   11.60   16.50   25.00
//
H VOGG950101
D (Vogt et al., 1995)
R PMID:7602593
A Vogt G, Etzold T, Argos P
T An assessment of amino acid exchange matrices in aligning protein sequences:
  the twilight zone revisited
J J. Mol. Biol. 249, 816-831 (1995)
M rows = ARNDCQEGHILKMFPSTWYV, cols = ARNDCQEGHILKMFPSTWYV
     7.6
     4.6     9.9
     4.9     5.5     9.0
     4.9     4.9     7.4     9.9
     5.7     3.0     3.4     2.0    16.7
     5.0     6.7     5.9     6.1     2.8     7.9
     5.2     5.6     6.1     7.9     2.2     6.9     8.8
     5.7     4.2     5.6     5.3     3.2     4.2     4.4    11.8
     4.4     5.8     6.4     5.6     3.9     6.4     5.6     3.8    11.2
     4.4     2.8     2.4     1.4     4.1     3.3     2.5     0.7     3.0     9.2
     4.0     3.0     2.2     1.2     3.7     3.6     2.4     0.8     3.3     8.0     9.2
     4.8     7.9     6.0     5.7     2.4     6.7     6.4     4.1     5.8     3.1     3.1     8.4
     4.5     3.5     3.0     2.2     4.3     4.2     3.2     1.7     3.9     7.7     8.0     3.8     9.5
     2.9     2.0     2.1     0.7     4.4     2.6     1.3     0.0     5.1     6.2     7.2     1.9     6.8    12.2
     5.5     4.3     4.3     4.5     2.1     5.0     4.7     3.6     4.1     2.6     2.9     4.6     2.8     1.4    12.8
     6.3     5.0     6.1     5.7     5.3     5.4     5.4     5.6     5.0     3.4     3.1     5.3     3.8     2.4     5.6     7.4
     5.8     5.0     5.7     5.2     4.7     5.2     5.1     4.1     4.9     4.6     3.9     5.3     4.6     3.0     5.3     6.7     7.7
     1.6     3.6     1.6     0.0     4.2     2.5     0.9     1.2     4.4     3.4     4.5     1.7     4.2     8.8     0.2     1.9     1.7    19.4
     3.0     3.4     3.8     2.4     4.7     3.5     2.5     1.2     7.4     4.5     5.2     3.1     5.0    10.3     2.1     3.3     3.3     9.3    13.0
     5.3     3.2     3.0     2.3     5.2     3.7     3.3     1.9     3.2     8.3     7.0     3.5     6.8     5.3     3.4     4.2     5.2     2.6     4.1     8.6
//
H KOSJ950101
D Context-dependent optimal substitution matrices for exposed helix
  (Koshi-Goldstein, 1995)
R PMID:8577693
A Koshi, J.M. and Goldstein, R.A.
T Context-dependent optimal substitution matrices.
J Protein Engineering 8, 641-645 (1995)
M rows = -ARNDCQEGHILKMFPSTWYV, cols = -ARNDCQEGHILKMFPSTWYV
   55.7    3.0    3.0    3.0    3.0    0.4    0.1    3.0    3.0    2.1    3.0    3.0    3.0    0.1    1.9    2.2    2.4    3.0    0.8    1.3    3.0
   25.6   47.2    1.5    1.0    0.7    0.3    1.9    2.3    4.3    0.6    0.2    2.0    0.8    0.1    0.3    3.1    2.8    3.7    0.4    0.1    2.0
   14.8    0.9   62.7    1.3    0.4    0.3    4.6    0.3    0.1    1.9    0.5    2.2    5.1    0.6    0.2    0.4    1.9    1.5    0.4    0.2    0.3
   15.2    0.2    0.5   48.2    3.3    0.1    3.2    4.9    0.1    1.7    1.7    1.4    3.0    0.6    1.0    0.1    9.7    2.7    0.7    1.1    1.5
   15.9    3.9    1.4    7.3   52.1    0.3    0.9   11.0    2.0    0.4    0.6    0.1    0.6    0.5    0.1    0.6    2.9    0.1    0.1    0.1    0.1
    9.4    1.5    0.1    1.5    1.6   73.6    0.1    2.6    0.1    0.1    2.1    4.0    0.1    0.1    0.8    0.7    0.3    2.2    0.1    0.1    0.1
    0.1    8.4    5.7    2.0    4.5    0.3   47.5    8.2    0.9    1.6    0.1    3.4    7.8    0.5    0.1    0.7    5.3    2.2    0.2    0.7    0.5
    5.2    5.3    1.0    1.5    8.6    0.1    4.9   56.8    1.5    1.0    0.3    0.9    5.8    0.1    0.2    1.6    2.1    2.4    0.2    0.1    1.1
   20.2    2.0    1.2    2.3    3.3    0.1    0.4    0.1      6    4.8    0.8    0.1    0.1    1.4    0.3    0.6    0.1    1.2    0.6    0.1    0.5
   13.3    0.3    4.7    7.5    1.8    0.1    4.4    0.7    0.1   56.9    0.6    0.1    2.3    1.2    2.2    0.1    0.1    0.1    0.1    4.4    0.1
   18.4    0.1    0.1    0.1    0.1    0.1    0.4    0.1    0.1    0.1      5    2.6   10.8    1.2    3.5    1.3    0.1    0.1    3.4    0.1    0.1
   15.4    0.8    0.6    0.1    0.1    0.1    1.1    0.1    0.2    0.2    3.4   67.3    0.6    3.5    3.5    0.1    0.1    0.7    0.1    0.1    2.9
    5.5    4.1    8.3    3.5    1.3    0.1    3.7    5.8    1.1    1.2    0.3    1.0   55.3    0.4    0.1    0.2    2.7    3.7    0.1    0.2    1.9
    0.7    5.2    4.3    3.2    0.1    0.5    2.0    5.4    1.5    0.1    7.4    9.3    3.0   44.0    1.3    0.1    2.4    4.3    0.1    0.1    6.0
   14.3    1.7    0.1    0.3    0.5    1.0    0.8    0.5    0.1    0.1    0.7    1.5    0.1    0.4   67.6    0.1    2.1    1.8    0.1    7.1    0.1
   13.6    1.7    1.0    0.5    3.1    0.1    0.6    0.6    0.1    1.0    0.8    1.5    2.7    0.1    0.1   65.9    5.2    1.8    0.1    0.3    0.2
    6.0   18.1    1.2    1.6    2.7    0.9    0.4    2.4    5.0    1.1    0.6    0.2    3.5    0.1    0.1    0.5   46.8    7.5    0.1    0.5    1.4
   18.4    7.5    0.3    2.5    0.7    0.1    0.4    0.2    1.8    0.8    2.4    4.8    1.2    1.0    0.1    0.2    6.3   48.8    0.1    0.6    2.7
   21.7    0.3    0.1    0.1    0.1    0.1    1.8    0.1    0.1    0.1    0.1    2.1    2.5    0.1    4.3    0.1    0.1    0.6   64.6    2.3    0.1
    8.3    0.5    0.1    0.1    0.1    0.1    0.1    1.1    0.1    3.4    2.4    6.6    0.9    0.2    8.7    0.3    0.9    1.5    1.0   60.8    3.8
   14.2    6.2    1.4    0.7    0.1    0.1    0.1    0.3    0.3    0.1   17.5    1.9    0.1    0.1    1.6    0.2    0.1    0.6    0.3    1.2   53.9
//
H KOSJ950102
D Context-dependent optimal substitution matrices for exposed beta
  (Koshi-Goldstein, 1995)
R PMID:8577693
A Koshi, J.M. and Goldstein, R.A.
T Context-dependent optimal substitution matrices.
J Protein Engineering 8, 641-645 (1995)
M rows = -ARNDCQEGHILKMFPSTWYV, cols = -ARNDCQEGHILKMFPSTWYV
   72.6    0.8    3.0    0.1    2.3    0.3    1.9    1.3    0.8    0.1    0.3    2.3    3.0    0.5    0.8    1.6    3.0    1.5    0.1    0.8    3.0
    7.5   60.3    2.2    0.1    1.6    1.1    0.6    1.6    0.4    0.1    0.8    2.9    1.0    0.7    0.1    2.0    6.2    4.8    0.1    1.6    5.1
   14.3    1.2   60.9    0.1    1.1    0.1    5.1    2.5    1.1    0.4    0.7    0.1    9.4    0.1    0.6    0.6    0.8    0.1    0.2    0.9    0.5
    3.0    2.1    3.0   53.5   11.8    0.1    2.9    0.1    1.8    2.5    0.1    1.3    4.4    0.1    0.3    1.2    9.0    1.6    0.1    1.9    0.1
   14.6    1.9    0.1    6.1   58.5    0.1    2.8    5.8    4.0    0.1    0.9    0.1    1.7    0.3    0.5    0.9    1.9    0.1    0.1    0.8    0.1
   20.4    1.9    0.1    0.1    1.7   49.5    1.6    0.1    1.7    0.1    4.0    0.1    0.1    0.1    8.4    0.1    2.0    1.9    0.1    3.9    3.5
   11.8    1.3    2.3    0.1    1.0    0.1   55.8    7.5    1.4    2.5    1.1    2.3    3.8    0.1    0.1    0.8    2.5    3.7    0.3    0.4    1.9
    5.0    1.5    0.6    1.7    8.4    0.1    2.0   66.4    0.6    1.1    0.5    0.7    4.2    0.1    0.1    0.6    3.3    1.5    0.4    0.1    2.0
    6.7    2.7    0.1    0.1    0.1    0.1    0.1    1.0   82.8    0.1    0.1    0.6    0.6    0.4    0.8    0.1    1.8    2.8    0.1    0.1    0.1
    0.1    1.2   10.0    5.7    0.1    0.7    0.3    4.2    0.8   45.8    0.1    1.7    1.8    1.3    0.1    0.1    8.3   10.8    0.1    4.6    2.8
    0.1    0.1    2.5    0.5    0.1    0.5    0.1    0.1    0.1    0.1   54.4    5.4    1.1    2.9    4.5    0.3    0.1    3.9    0.1    1.5   22.8
   14.2    1.0    0.6    0.7    0.1    0.1    2.1    0.5    0.1    1.8    5.7   60.3    0.9    2.6    2.9    1.7    1.2    0.1    0.1    0.7    3.4
    7.9    1.6    8.1    2.1    0.4    0.7    3.3    2.4    0.3    0.7    0.8    1.3   61.5    0.1    0.6    0.5    2.6    4.6    0.3    0.1    0.9
   12.6    6.3    3.2    0.1    0.1    0.1    2.7    2.6    0.1    0.1    4.9    2.3    7.8   46.5    1.0    0.1    3.9    2.2    0.1    0.1    4.2
    8.2    0.1    0.1    0.6    0.1    0.1    0.1    0.1    1.0    1.1    2.1    1.9    0.1    2.1   66.1    0.1    2.1    0.6    0.9   10.5    2.9
   16.8    6.2    0.1    0.6    0.7    0.1    0.7    0.1    0.8    0.1    0.1    1.3    0.5    0.1    0.1   67.1    2.7    2.5    0.1    0.3    0.1
   30.0    2.0    0.1    1.7    0.1    0.1    0.1    1.0    4.6    0.5    0.2    0.7    0.9    0.1    0.1    2.8   49.8    4.5    0.1    0.1    1.5
    4.7    3.4    1.5    2.0    2.6    0.1    0.4    3.9    0.6    0.1    1.8    1.4    4.7    0.1    0.1    0.1    8.4   59.0    0.3    0.5    5.0
    5.9    0.1    0.1    0.1    0.1    0.1    0.1    2.3    2.0    0.1    0.8    2.9    0.1    0.1    4.7    0.1    1.0    0.1   75.5    2.9    2.5
    5.0    2.1    0.9    1.1    0.1    0.1    0.5    0.4    0.1    2.7    3.0    2.7    0.8    0.1    5.9    0.1    1.6    0.1    0.7   72.2    0.8
   18.1    1.2    0.5    0.1    0.4    0.1    2.0    2.3    1.1    0.1    6.9    4.6    0.1    2.1    0.8    0.9    0.4    1.0    0.1    0.4   57.5
//
H KOSJ950103
D Context-dependent optimal substitution matrices for exposed turn
  (Koshi-Goldstein, 1995)
R PMID:8577693
A Koshi, J.M. and Goldstein, R.A.
T Context-dependent optimal substitution matrices.
J Protein Engineering 8, 641-645 (1995)
M rows = -ARNDCQEGHILKMFPSTWYV, cols = -ARNDCQEGHILKMFPSTWYV
   69.2    3.0    1.3    3.0    0.9    0.7    1.9    3.0    3.0    1.6    0.9    1.3    0.8    0.6    1.1    1.4    1.0    3.0    0.1    1.4    0.8
   31.5   46.2    1.1    0.8    0.8    0.1    0.3    0.3    2.5    0.1    2.0    2.3    0.9    0.4    0.3    0.2    4.4    2.0    0.4    0.1    4.1
    5.9    1.3   64.3    2.5    1.7    0.5    2.6    0.1    2.4    2.1    0.2    0.2    8.7    0.4    0.4    0.6    3.5    1.2    0.6    0.5    1.1
    9.3    1.7    1.2   55.1    6.4    0.5    1.3    1.7    4.4    0.8    0.1    0.4    3.8    0.7    0.3    0.2    8.9    1.3    0.3    1.4    1.0
    2.1    2.9    0.2    9.4   61.5    0.1    1.9    9.2    3.4    0.4    0.1    0.6    3.1    0.1    0.1    1.4    2.5    1.4    0.1    0.2    0.3
   17.0    7.1    0.1    0.1    0.1   66.1    0.1    0.1    2.0    0.8    0.4    0.7    0.1    0.3    3.0    0.1    2.6    0.1    0.1    0.3    0.1
    9.0    4.9    3.9    3.3    2.3    0.1   48.8    4.8    1.7    2.0    1.6    4.3    4.7    0.8    0.4    2.1    1.6    3.3    0.1    0.1    0.9
    7.8    3.8    1.0    1.1    7.0    0.1    3.5   57.8    1.1    1.5    1.1    1.7    4.5    0.4    0.4    1.7    3.3    1.0    0.4    0.3    1.0
    6.5    2.8    0.4    2.9    2.8    0.1    0.8    1.9   74.8    0.4    0.1    0.1    1.7    0.1    0.4    0.3    2.2    1.9    0.1    0.1    0.3
   14.9    1.8    0.1    4.0    0.1    0.6    2.9    1.4    0.7   56.0    0.6    0.4    2.9    0.2    2.8    2.2    2.2    0.1    0.9    5.9    0.1
   10.4    0.1    0.1    0.1    0.1    0.5    0.1    0.1    0.1    0.1   65.5    7.0    0.1    2.4    0.8    0.5    0.1    2.7    0.7    0.9    8.8
    9.1    0.7    3.1    0.3    0.1    0.1    0.1    0.7    0.3    0.4    3.7   68.3    0.8    4.4    1.7    0.6    0.3    1.0    1.0    1.3    2.8
    2.5    4.7    8.1    2.6    1.3    0.1    5.9    4.4    1.3    1.6    0.1    1.4   58.1    0.5    0.5    0.5    2.9    2.0    0.1    0.5    1.5
   15.2    1.3    0.8    0.1    0.1    0.4    0.1    0.1    0.1    0.6    4.7    6.8    0.8   61.0    2.9    0.1    0.1    1.1    0.1    2.8    1.8
   14.8    0.1    0.8    0.7    0.1    0.4    0.4    0.1    0.1    0.1    0.6    3.5    0.9    0.7   70.0    0.7    0.1    0.1    2.9    2.4    1.5
    4.4    7.5    1.7    1.0    1.2    0.1    0.4    2.2    0.7    0.4    0.9    0.8    2.3    0.4    0.1   70.2    3.0    2.4    0.1    0.2    0.6
    2.5   10.8    1.1    2.5    5.3    0.9    1.7    1.8    5.1    1.0    0.4    1.4    3.1    0.4    0.6    1.8   49.6    8.8    0.1    0.8    0.7
   15.3    2.9    1.3    2.9    1.5    0.1    1.5    1.5    0.9    0.2    2.0    1.0    1.9    0.6    0.1    0.5    9.5   54.0    0.3    0.1    2.8
   10.5    0.1    0.1    0.1    0.1    0.7    0.1    0.1    0.1    0.1    0.1    0.3    0.1    0.1    0.1    1.0    0.1    0.1   77.0   10.5    0.1
   13.0    0.1    0.4    0.1    0.1    0.1    0.1    0.7    0.1    0.9    1.2    2.8    0.5    0.1    8.4    0.3    0.1    0.4    0.1   71.2    0.5
    8.1    2.7    0.2    0.3    0.1    1.8    0.8    0.1    1.0    0.5   10.3    4.5    1.3    1.1    2.7    0.1    0.7    2.1    0.3    1.9   60.1
//
H KOSJ950104
D Context-dependent optimal substitution matrices for exposed coil
  (Koshi-Goldstein, 1995)
R PMID:8577693
A Koshi, J.M. and Goldstein, R.A.
T Context-dependent optimal substitution matrices.
J Protein Engineering 8, 641-645 (1995)
M rows = -ARNDCQEGHILKMFPSTWYV, cols = -ARNDCQEGHILKMFPSTWYV
   50.4    3.0    3.0    2.5    3.0    1.1    3.0    3.0    3.0    1.8    3.0    3.0    3.1    1.4    1.5    3.0    3.0    3.0    0.5    1.8    3.0
   29.8   49.8    0.1    0.5    0.8    0.1    2.1    0.3    4.1    0.6    0.5    1.1    0.3    0.1    0.1    2.2    3.7    1.4    0.2    0.1    3.1
   15.0    1.2   60.3    1.2    0.1    0.1    1.2    0.7    0.1    2.5    0.9    0.9    6.6    0.1    0.1    2.1    2.5    3.1    0.6    0.9    0.7
    8.3    1.6    2.6   50.6    5.5    0.5    2.0    3.2    2.2    2.7    0.9    1.0    4.7    0.9    0.3    0.1    6.8    3.9    0.1    1.2    1.4
    9.1    1.6    0.6    7.8   62.7    0.1    2.5    6.1    1.3    0.1    0.4    0.5    1.4    0.3    0.2    1.4    1.8    1.4    0.1    1.1    0.3
   23.2   12.9    0.2    0.1    1.5   58.1    0.1    1.2    0.1    0.1    2.0    0.1    0.1    0.8    0.1    0.1    0.1    0.3    0.1    0.1    0.1
   28.1    0.1    2.2    2.0    0.1    0.1   44.4    9.2    0.1    1.4    0.6    0.4    3.1    1.5    0.1    0.1    1.6    3.6    0.1    0.7    1.6
   22.2    5.1    0.5    0.5    4.3    0.1    3.0   57.1    1.4    0.7    0.5    0.6    1.1    0.1    0.1    0.1    1.6    0.9    0.1    0.1    1.0
   18.4    1.5    0.3    1.4    1.7    0.4    0.3    0.9   70.2    0.4    0.1    0.2    0.4    0.2    0.3    0.2    2.1    0.8    0.1    0.3    0.4
   27.6    1.2    0.5    0.1    4.2    0.1    2.6    1.0    0.1   50.8    0.1    0.1    1.9    0.3    0.9    3.9    4.8    0.1    0.1    0.9    0.1
   30.9    1.2    0.1    0.1    0.1    0.1    0.1    0.7    1.6    0.9   41.7    3.8    2.2    0.1    0.4    1.3    0.1    0.8    0.7    0.5   13.6
   18.9    0.7    1.0    0.4    0.2    0.3    2.1    0.4    0.4    0.6    6.0   57.6    0.1    3.3    3.8    1.3    0.1    0.5    0.1    0.1    2.9
    9.3    3.5    6.0    2.2    3.3    0.1    3.9    4.4    1.8    0.8    0.1    2.5   52.1    0.5    0.8    2.6    3.2    2.6    0.1    0.1    1.0
   22.9    0.1    0.1    0.1    0.1    0.1    0.1    0.3    0.1    1.0    7.9    9.1    1.0   45.8    2.2    1.7    0.1    6.3    0.1    0.1    2.2
   16.2    0.3    0.7    0.8    0.1    0.1    0.1    0.1    0.1    0.1    1.4    2.5    0.7    0.1   69.1    0.1    0.1    0.1    0.9    7.5    0.3
   15.4    6.7    0.8    0.2    0.3    0.1    1.3    2.0    1.3    0.2    0.1    0.6    0.4    0.1    0.1   64.2    3.6    0.6    0.1    0.7    1.9
   13.4    5.0    0.9    3.6    3.5    1.8    1.0    1.6    3.3    0.1    0.3    0.3    0.8    0.1    0.6    3.5   48.7    8.7    0.4    0.3    2.6
   16.3    4.5    0.1    2.3    0.6    0.4    1.7    0.5    0.6    0.4    2.4    1.9    1.0    0.1    0.6    2.6    8.9   51.4    0.1    0.4    4.0
   15.9    0.1    0.1    1.1    0.1    0.1    0.1    0.1    0.1    0.1    3.2    0.1    0.6    1.8    2.7    0.1    0.2    0.1   73.5    1.4    0.1
   15.5    0.4    0.1    0.1    0.1    0.1    0.1    0.1    0.6    0.6    0.1    2.5    0.1    0.6    8.4    0.1    0.1    0.6    1.0   68.7    1.6
   25.4    1.4    0.1    0.7    0.4    0.4    0.6    0.1    0.1    0.1    8.0    4.3    1.3    1.1    1.5    0.1    0.9    2.5    0.1    0.1   51.9
//
H KOSJ950105
D Context-dependent optimal substitution matrices for buried helix
  (Koshi-Goldstein, 1995)
R PMID:8577693
A Koshi, J.M. and Goldstein, R.A.
T Context-dependent optimal substitution matrices.
J Protein Engineering 8, 641-645 (1995)
M rows = -ARNDCQEGHILKMFPSTWYV, cols = -ARNDCQEGHILKMFPSTWYV
   61.0    3.0    1.8    4.0    1.7    3.0    2.3    0.5    3.0    0.1    3.0    3.6    0.5    3.0    1.7    0.9    1.9    3.0    0.5    0.8    0.6
    1.3   76.5    0.6    0.1    0.2    0.4    0.7    1.8    2.5    0.1    0.6    1.7    0.8    0.5    0.4    0.7    6.6    1.6    0.1    0.8    2.8
    2.6    1.3   79.9    0.6    0.1    0.3    3.1    1.3    0.1    1.2    0.1    0.9    4.6    0.1    0.4    0.5    2.6    0.9    0.1    0.3    0.1
    7.6    3.2    0.1   70.8    3.8    0.6    0.1    2.5    1.4    0.1    0.9    0.1    1.0    0.1    0.1    0.5    3.2    3.5    0.1    1.4    0.1
    3.1    2.9    0.4    1.2   78.5    0.1    0.1    5.6    0.1    0.1    0.4    0.6    2.0    0.1    0.3    1.1    2.3    0.9    0.1    0.8    0.1
    7.9    7.5    0.9    0.1    1.4   56.1    1.5    0.7    4.2    0.1    2.3    0.8    0.1    1.8    1.1    0.1    4.4    2.1    0.9    0.1    6.6
    4.3    2.9    1.7    2.6    2.8    0.1   74.3    1.5    0.3    3.4    0.1    0.1    3.2    0.9    0.1    0.5    0.5    1.1    0.5    0.1    0.1
    2.4    1.4    0.1    0.2    1.5    0.2    4.4   80.7    1.3    0.1    1.1    2.8    2.5    0.1    0.1    0.1    0.7    0.1    0.1    0.6    0.6
    2.3    7.0    0.8    1.3    0.5    0.2    1.3    1.8   80.3    0.3    0.1    0.3    0.7    0.1    0.1    0.1    1.6    1.1    0.1    0.1    0.9
    0.1    0.9    1.9    1.0    0.4    0.1    2.9    1.0    0.1   85.0    0.1    0.1    2.2    0.6    1.6    0.5    0.9    1.1    0.1    0.1    0.6
    1.9    1.1    0.7    0.3    0.2    0.1    0.1    0.2    0.5    0.1   75.2    7.3    0.3    2.3    1.3    0.1    0.5    1.8    0.2    0.4    6.3
    1.0    0.7    0.2    0.5    0.1    0.4    0.6    0.2    0.1    0.4    5.5   78.6    0.7    3.0    3.3    0.1    0.6    0.2    0.1    0.6    3.7
    1.5    0.1    5.3    3.4    0.1    0.1    0.9    2.8    0.8    0.1    0.1    4.2   73.1    2.3    0.1    0.1    1.1    1.5    0.1    1.4    2.0
    2.9    2.6    0.1    0.5    0.1    0.4    1.1    0.1    0.6    0.1    5.6   11.9    0.1   65.8    2.6    0.1    0.1    2.7    0.9    0.1    2.9
    1.2    0.4    0.1    0.1    0.3    0.1    0.1    0.2    0.2    0.4    0.5    6.5    0.1    0.5   78.0    0.3    0.3    0.5    2.9    7.1    1.0
    3.1    0.1    0.1    0.8    0.1    0.1    1.1    1.2    0.8    1.0    0.7    0.1    0.2    0.1    0.1   85.9    1.8    1.9    0.1    0.1    1.8
    2.2    4.9    1.0    2.7    0.1    2.1    1.8    0.1    2.7    0.1    0.6    0.6    0.1    0.6    0.8    0.3   73.5    5.8    0.1    0.1    0.6
    4.3    4.1    1.6    0.1    0.3    0.4    0.4    0.9    0.7    0.1    0.1    2.2    1.0    0.5    0.5    1.1    5.2   72.1    0.1    0.1    5.0
    1.0    0.3    0.4    0.1    1.1    0.1    0.1    0.1    0.1    0.1    0.1    1.2    1.7    0.1    0.1    0.4    0.7    0.1   91.3    1.2    1.2
    0.9    1.4    0.8    0.8    0.1    0.6    0.2    0.6    0.1    2.3    0.5    4.3    0.7    1.4    8.2    0.1    0.6    0.3    0.4   76.6    0.1
    0.3    7.2    0.6    0.2    0.4    0.8    0.4    0.5    0.1    0.4   13.4    5.9    0.1    2.2    0.6    0.1    0.1    3.1    0.1    0.1   64.2
//
H KOSJ950106
D Context-dependent optimal substitution matrices for buried beta
  (Koshi-Goldstein, 1995)
R PMID:8577693
A Koshi, J.M. and Goldstein, R.A.
T Context-dependent optimal substitution matrices.
J Protein Engineering 8, 641-645 (1995)
M rows = -ARNDCQEGHILKMFPSTWYV, cols = -ARNDCQEGHILKMFPSTWYV
   56.4    3.0    2.1    1.7    1.6    3.0    1.7    2.1    3.0    0.9    3.0    3.0    1.1    1.1    2.0    3.0    3.0    3.0    0.7    1.7    3.0
    5.8   66.6    0.5    0.9    1.5    0.3    0.6    1.7    3.7    1.0    0.4    0.3    1.0    0.1    0.1    2.6    7.3    3.7    0.1    0.2    2.4
   16.1    0.1   72.6    0.1    0.1    0.1    0.8    0.1    2.5    0.1    0.7    1.0    3.0    0.8    0.1    0.9    0.1    2.0    0.1    0.1    0.1
    9.5    0.1    1.5   70.8    4.2    0.1    1.3    0.1    1.2    1.6    0.5    0.1    2.8    0.1    0.1    1.1    2.6    1.9    0.7    0.1    0.8
   11.0    0.1    0.2    2.9   80.8    0.1    0.2    1.0    1.2    0.1    0.6    0.9    0.1    0.1    0.1    0.1    0.6    1.3    0.1    0.1    0.1
   12.4    5.9    0.4    0.4    0.8   65.6    0.1    0.8    1.2    0.7    2.5    3.0    0.1    0.4    1.2    0.5    3.0    1.9    0.1    0.1    0.1
   10.9    0.1    3.1    1.9    0.1    0.1   71.6    3.3    0.1    0.1    0.1    3.0    2.6    1.4    0.4    0.6    0.1    0.6    0.1    0.7    0.5
   14.3    0.9    1.2    1.0    4.4    0.1    2.3   67.9    2.3    0.1    0.1    0.7    1.7    0.1    0.4    0.1    0.2    0.1    0.1    1.0    2.3
    5.8    2.8    0.1    0.1    0.7    0.1    0.1    0.1   87.6    0.6    0.1    0.1    0.1    0.1    0.1    0.3    1.4    0.3    0.1    0.1    0.4
    6.3    0.1    5.0    1.3    2.2    0.6    3.0    2.5    0.1   70.9    0.1    1.6    0.5    0.9    1.0    0.5    2.3    0.1    0.9    1.1    0.1
    3.2    0.4    0.4    0.3    0.1    0.4    0.1    0.1    0.1    0.1   64.4    8.9    0.2    2.0    2.3    0.4    0.7    1.6    0.4    0.3   14.4
    5.8    0.6    0.1    0.1    0.1    0.2    0.1    0.3    0.3    0.1    4.4   77.6    0.1    2.8    2.2    0.2    0.1    0.3    0.3    0.8    4.4
   11.0    0.6   10.7    0.1    0.1    0.1    2.2    0.2    0.1    1.5    1.5    0.7   67.7    0.1    0.1    0.4    0.7    1.7    0.1    0.4    0.9
    4.9    3.1    0.1    0.6    0.4    0.6    2.8    0.1    0.5    0.1    4.4    9.4    0.1   63.4    3.1    0.7    0.1    2.5    0.1    0.5    3.6
    3.4    0.2    0.1    0.1    0.1    0.3    0.1    0.1    0.3    0.4    2.4    3.0    0.2    1.1   79.7    0.1    0.6    0.7    1.2    5.2    1.7
   16.2    1.8    0.5    0.1    0.1    0.1    1.3    0.7    0.5    0.1    0.1    0.3    0.7    0.1    0.1   73.3    4.4    0.8    0.1    0.1    0.1
   13.9    2.5    3.0    2.8    1.1    0.3    1.1    1.4    3.7    0.5    0.1    0.1    0.8    0.5    0.8    0.9   63.3    3.4    0.1    0.1    0.5
    8.9    2.9    0.4    0.7    0.1    0.4    1.0    1.8    0.6    0.3    2.0    0.6    1.6    0.7    0.1    0.4    4.6   70.2    0.1    0.7    2.5
    4.6    0.1    0.6    0.1    0.1    0.2    0.1    0.1    0.1    0.1    0.1    0.1    0.1    0.6    1.2    0.1    0.5    0.1   90.5    2.2    0.1
    4.0    0.1    0.6    1.5    0.1    1.0    0.3    0.1    0.1    1.3    0.5    0.7    0.4    0.1    6.3    0.6    1.1    0.6    0.8   80.9    0.1
    3.9    2.4    0.3    0.1    0.4    0.8    0.2    0.1    0.1    0.1    9.6    3.0    0.1    0.2    0.6    0.3    1.1    2.1    0.1    0.3   75.0
//
H KOSJ950107
D Context-dependent optimal substitution matrices for buried turn
  (Koshi-Goldstein, 1995)
R PMID:8577693
A Koshi, J.M. and Goldstein, R.A.
T Context-dependent optimal substitution matrices.
J Protein Engineering 8, 641-645 (1995)
M rows = -ARNDCQEGHILKMFPSTWYV, cols = -ARNDCQEGHILKMFPSTWYV
   86.4    1.4    0.7    0.4    1.5    0.5    0.6    0.1    2.5    0.1    0.1    0.5    0.2    0.2    0.8    0.6    0.5    0.7    0.1    0.5    1.7
    2.6   65.6    0.8    2.3    0.7    0.1    0.5    2.0    7.6    1.3    1.2    2.7    0.1    0.4    0.1    3.2    0.8    4.5    0.1    0.1    4.4
    4.1    1.7   81.2    1.2    0.1    0.6    2.8    0.6    0.1    0.8    0.7    0.1    3.6    0.1    0.1    0.6    0.1    1.1    0.1    0.6    0.7
    1.5    1.0    1.9   79.8    5.0    0.1    0.6    0.2    3.5    2.1    0.1    1.1    1.1    0.1    0.3    0.1    2.2    0.1    0.1    0.1    0.2
    5.2    0.1    0.4    3.1   78.1    0.1    0.1    4.0    1.7    1.5    0.1    1.3    0.1    0.4    0.1    0.7    1.9    0.5    0.1    0.9    0.8
    3.3    9.5    0.1    0.1    4.0   73.0    0.1    2.3    2.9    0.1    0.1    0.1    0.1    0.1    1.5    0.7    1.9    0.1    0.1    0.1    1.2
    3.9    0.1    2.9    0.1    0.1    0.1   70.3    4.6    2.7    4.6    0.9    0.1    4.7    1.8    0.1    3.3    0.1    0.1    0.7    0.1    0.1
    0.1    2.2    0.1    1.4    9.3    0.1    3.8   71.2    0.3    0.1    0.1    0.1    3.4    0.1    0.1    3.0    1.2    3.2    0.1    0.1    1.5
    2.2    1.6    0.3    0.3    0.7    0.1    0.1    0.3   91.5    0.1    0.1    0.3    1.0    0.1    0.1    0.1    1.6    0.1    0.1    0.1    0.1
    0.7    1.0    0.1    0.1    0.1    0.1    0.1    1.2    0.1   85.1    0.1    0.1    0.9    1.7    2.6    2.8    1.2    1.2    0.1    1.9    0.1
    0.7    0.1    0.1    1.2    0.1    0.1    0.2    0.5    0.1    0.1   76.1    7.3    0.4    4.0    1.2    0.1    0.1    1.9    0.1    0.1    6.9
    0.8    1.6    1.0    0.1    0.4    0.4    2.4    0.6    0.5    0.9    5.8   75.9    0.5    3.1    2.9    0.1    0.1    0.4    0.1    0.4    3.0
    0.1    1.0    5.8    5.9    1.1    0.1    2.6    0.1    1.7    0.1    0.1    0.1   76.7    1.1    0.1    0.1    0.6    3.9    0.1    0.1    0.1
    0.1    0.1    1.0    0.6    0.1    0.2    0.1    1.7    0.1    0.1    2.4    8.3    0.8   78.9    3.0    0.1    0.1    0.1    0.1    0.1    3.5
    1.7    0.3    0.1    0.5    0.1    0.1    0.1    0.1    0.1    0.8    0.7    2.7    0.3    1.1   81.2    0.1    1.2    0.1    1.3    6.7    2.1
    1.5    1.7    0.3    0.9    0.1    0.1    0.5    0.1    0.6    0.1    0.6    1.4    0.1    0.1    0.1   90.7    1.8    0.3    0.1    0.1    0.1
    1.4   14.2    1.8    1.7    4.3    1.1    1.5    1.0    0.1    0.9    0.9    0.8    1.7    0.1    0.1    0.1   67.3    0.8    0.1    1.0    0.1
    1.6    1.1    0.1    2.6    0.4    1.3    0.1    0.1    1.1    0.1    0.9    0.1    0.7    1.5    0.3    2.6   11.7   72.3    0.1    0.1    2.3
    2.1    0.1    0.1    0.1    0.1    0.7    0.1    0.1    0.6    0.1    0.9    0.3    0.1    1.3    1.8    0.1    1.2    0.7   88.7    1.5    0.7
    2.0    0.5    0.1    1.6    0.1    0.4    0.8    0.7    0.1    4.9    0.3    1.3    0.4    0.1    6.5    0.1    0.1    1.1    0.1   79.7    0.1
    4.0    5.1    0.1    1.1    0.5    0.1    1.1    0.1    0.1    0.1    7.0    6.2    0.1    0.1    1.7    1.4    0.8    3.2    0.3    0.8   67.2
//
H KOSJ950108
D Context-dependent optimal substitution matrices for buried coil
  (Koshi-Goldstein, 1995)
R PMID:8577693
A Koshi, J.M. and Goldstein, R.A.
T Context-dependent optimal substitution matrices.
J Protein Engineering 8, 641-645 (1995)
M rows = -ARNDCQEGHILKMFPSTWYV, cols = -ARNDCQEGHILKMFPSTWYV
   74.9    3.0    0.2    0.6    2.2    1.2    1.5    1.4    1.5    0.4    0.8    2.5    0.7    0.5    1.0    1.6    1.7    0.9    0.1    0.7    2.5
    7.2   68.0    0.6    0.5    0.5    1.0    0.2    0.1    5.5    0.1    0.4    0.5    0.9    0.5    0.4    1.8    5.7    4.4    0.1    0.1    2.1
    4.0    0.1   77.6    0.7    0.1    0.5    1.7    0.4    0.1    3.1    0.1    3.6    1.3    0.1    1.0    0.1    4.5    2.0    0.1    0.1    0.1
    2.4    0.1    0.1   83.8    3.0    0.4    1.2    0.1    2.5    1.4    0.3    0.1    1.1    0.3    0.1    0.1    2.5    0.5    0.1    0.1    0.9
    7.4    1.7    0.4    4.7   75.7    0.1    0.1    3.0    0.2    0.5    1.0    0.3    0.5    0.1    0.1    0.9    1.9    0.4    0.1    1.8    0.1
    5.3    9.2    0.1    1.2    0.1   64.4    0.7    1.4    1.4    0.1    1.4    1.3    0.1    3.2    2.0    0.1    3.5    0.8    1.2    2.1    1.4
   11.0    2.6    2.6    0.1    3.8    0.1   61.4    2.8    1.9    0.1    0.1    1.9    2.2    0.9    0.7    1.8    3.5    2.4    0.1    0.9    0.1
   13.1    1.4    2.8    0.1    0.8    0.1    3.6   70.2    2.2    1.8    0.1    0.1    2.4    0.1    0.1    1.1    0.1    0.1    0.1    0.9    0.1
    2.4    0.5    0.1    0.5    1.1    0.1    0.4    0.5   91.6    0.1    0.1    0.1    0.1    0.1    0.1    0.6    1.9    0.5    0.1    0.3    0.1
    2.2    0.6    0.2    2.9    1.4    1.2    0.7    0.1    0.1   84.6    0.7    1.1    0.1    0.1    1.6    0.1    0.1    0.1    0.1    3.2    0.1
    1.9    0.1    0.4    0.1    0.4    0.1    0.3    0.6    0.7    0.1   71.1    7.6    0.1    1.4    1.5    0.1    0.7    0.8    0.3    0.1   12.5
    4.1    0.8    0.2    0.1    0.1    0.3    1.2    0.2    0.1    0.5    4.0   78.4    0.6    2.9    2.8    0.7    0.2    0.6    0.1    0.8    2.4
    6.3    0.8    7.1    1.5    0.1    0.1    0.1    0.2    5.1    2.1    1.4    0.1   71.1    0.1    0.1    0.8    1.1    0.1    0.1    0.1    3.0
    4.2    0.4    0.1    0.1    0.8    0.1    0.1    0.1    0.1    0.6    6.8    9.9    0.1   69.7    0.1    0.1    1.4    0.1    0.1    0.1    6.5
    2.8    0.1    0.1    0.1    0.1    0.1    0.5    0.1    0.5    0.5    1.1    4.1    0.1    0.7   78.6    1.1    1.1    0.7    0.7    5.7    2.0
    2.9    3.7    0.5    1.1    0.1    0.1    1.1    0.9    0.3    0.2    1.7    0.7    0.1    0.8    0.1   83.5    1.9    0.4    0.1    0.1    0.7
    4.1    4.0    0.4    2.6    1.9    1.4    0.2    1.5    1.8    0.8    0.4    0.4    0.7    0.1    0.2    2.8   70.2    5.4    0.1    1.2    0.5
    2.2    1.4    0.4    2.6    0.8    0.8    1.3    0.8    1.3    0.7    0.9    0.1    0.9    0.7    0.1    0.7    5.3   76.9    0.1    0.5    2.3
    0.1    0.1    0.9    0.1    0.1    0.1    0.1    0.1    0.1    0.1    2.2    1.7    0.9    0.1    6.9    0.1    0.1    0.1   82.1    4.2    1.5
    2.7    0.1    0.6    0.6    0.1    0.1    0.1    0.1    0.5    1.7    0.7    1.0    0.5    0.3    8.8    0.1    0.1    0.1    0.1   82.2    0.6
    4.4    4.3    0.2    1.1    0.2    1.2    0.1    0.6    0.5    0.1    6.0    3.8    0.7    0.1    1.3    0.7    2.1    3.2    0.2    0.5   69.4
//
H KOSJ950109
D Context-dependent optimal substitution matrices for alpha helix
  (Koshi-Goldstein, 1995)
R PMID:8577693
A Koshi, J.M. and Goldstein, R.A.
T Context-dependent optimal substitution matrices.
J Protein Engineering 8, 641-645 (1995)
M rows = -ARNDCQEGHILKMFPSTWYV, cols = -ARNDCQEGHILKMFPSTWYV
   70.7    1.7    2.1    2.5    2.0    2.2    1.8    0.7    2.7    1.7    1.9    1.1    0.3    0.8    1.0    2.4    0.2    2.6    1.1    0.3    0.1
    9.1   63.1    0.9    0.5    1.1    0.9    1.2    2.2    3.5    0.2    0.3    1.4    1.8    0.8    0.3    1.1    6.4    2.6    0.2    0.4    2.3
   11.4    1.2   68.9    1.0    0.3    0.2    3.0    0.4    0.2    1.4    0.4    1.4    5.1    0.4    0.2    0.6    1.7    1.1    0.3    0.3    0.6
   13.8    1.8    0.6   60.2    3.7    0.2    1.4    3.7    0.9    1.2    0.9    0.4    2.0    0.7    0.5    0.1    4.0    1.8    0.3    1.1    0.8
   11.0    2.7    1.1    4.1   61.0    0.3    0.5    9.8    1.4    0.5    0.4    0.4    1.6    0.3    0.3    1.2    2.0    1.0    0.2    0.3    0.0
   12.3    3.5    0.0    0.7    1.3   66.6    0.1    1.8    1.5    0.0    1.2    1.3    0.0    0.9    0.9    0.4    2.6    1.7    0.3    0.1    2.8
   10.1    3.3    4.1    2.0    1.6    0.3   61.3    3.7    0.4    2.2    0.0    1.9    3.6    0.4    0.3    0.8    2.1    0.5    0.5    0.5    0.5
    3.9    4.0    1.1    1.5    6.6    0.4    6.0   61.5    1.4    0.8    0.4    1.1    4.8    0.3    0.1    1.1    2.2    1.7    0.1    0.2    0.9
   15.0    3.7    1.0    1.2    1.4    0.4    0.8    1.1   69.8    0.4    0.1    0.4    0.9    0.3    0.4    0.3    1.2    0.7    0.0    0.3    0.8
    9.4    0.4    4.2    4.9    1.4    0.0    3.4    1.0    0.1   65.5    0.5    0.1    2.5    0.6    1.7    0.2    0.4    1.4    0.0    2.0    0.5
   10.7    0.6    0.3    0.4    0.1    0.3    0.1    0.4    0.3    0.1   65.9    6.9    0.5    2.1    1.5    0.2    0.3    1.6    0.0    0.3    7.3
    6.3    0.7    0.6    0.5    0.1    0.3    0.7    0.3    0.1    0.3    4.9   72.6    1.0    2.9    2.9    0.2    0.3    0.7    0.2    1.1    3.2
    1.6    3.1    8.0    3.2    1.7    0.1    4.3    6.0    1.1    1.1    0.5    1.4   58.5    1.0    0.0    0.5    2.3    3.1    0.5    0.4    1.7
    4.2    3.3    0.3    0.6    0.1    0.4    1.6    1.3    1.1    0.1    5.8   11.8    0.2   58.3    1.8    0.0    1.0    3.1    0.7    0.2    4.1
    5.5    1.1    0.0    0.3    0.3    0.3    0.4    0.3    0.1    0.4    0.5    5.5    0.0    0.6   72.9    0.3    0.8    0.9    2.2    6.7    1.0
   13.6    1.5    0.8    0.6    1.8    0.1    0.7    0.8    0.5    1.0    0.9    0.9    2.0    0.0    0.1   69.1    3.1    1.4    0.3    0.1    0.8
    0.8    9.5    2.0    3.8    2.3    1.4    2.5    2.1    3.7    1.5    0.8    0.9    1.7    0.4    0.4    0.8   56.3    7.9    0.2    0.4    0.7
   14.6    3.8    0.9    1.4    0.4    0.4    0.4    0.6    1.0    0.5    1.4    2.7    1.4    0.8    0.3    1.2    4.7   59.9    0.0    0.4    3.5
    6.1    0.7    0.2    0.1    0.9    0.1    0.1    0.0    0.0    0.0    0.0    1.0    2.2    0.2    0.5    0.1    0.6    0.0   84.5    1.7    1.1
    1.9    1.1    0.4    0.6    0.1    0.6    0.1    1.0    0.1    3.0    1.1    4.6    0.9    1.0    9.0    0.0    0.9    0.6    0.5   71.7    0.9
    0.8    8.5    0.7    0.4    0.1    0.8    0.3    0.9    0.2    0.3   15.1    5.9    0.4    1.7    0.8    0.2    0.2    2.8    0.3    0.8   58.9
//
H KOSJ950110
D Context-dependent optimal substitution matrices for beta sheet
  (Koshi-Goldstein, 1995)
R PMID:8577693
A Koshi, J.M. and Goldstein, R.A.
T Context-dependent optimal substitution matrices.
J Protein Engineering 8, 641-645 (1995)
M rows = -ARNDCQEGHILKMFPSTWYV, cols = -ARNDCQEGHILKMFPSTWYV
   68.7    1.0    2.7    1.2    2.0    3.0    2.1    1.7    1.1    1.0    0.7    1.4    1.4    1.3    0.7    2.9    2.9    1.3    1.0    0.8    1.1
    5.8   64.6    1.1    1.0    1.3    1.1    0.5    1.8    3.0    0.8    0.2    0.7    0.8    1.1    0.1    2.2    6.7    3.8    0.0    0.6    3.0
   15.4    0.3   66.4    0.4    0.9    0.0    3.8    1.2    1.8    1.2    0.5    0.3    4.5    0.5    0.3    0.8    1.0    0.4    0.1    0.2    0.2
    6.7    0.2    1.8   63.9    7.6    0.1    1.9    0.3    1.3    2.1    0.3    0.9    3.4    0.2    0.1    1.4    4.8    1.4    0.0    0.9    0.7
   11.6    1.1    0.2    3.8   70.5    0.3    0.9    4.5    2.0    0.2    0.5    0.3    1.1    0.0    0.4    0.3    0.9    0.6    0.0    0.5    0.4
   17.0    4.6    0.0    0.4    1.1   62.5    0.0    0.3    1.3    0.5    2.6    2.2    0.1    0.2    2.3    0.0    2.7    1.5    0.0    0.2    0.6
   12.2    1.0    1.6    1.3    0.7    0.0   63.2    5.4    0.6    0.9    0.3    2.8    3.1    1.2    0.2    0.5    0.9    1.9    0.5    0.6    1.2
    9.6    1.3    0.8    1.4    5.6    0.1    2.2   66.1    1.3    0.8    0.4    0.7    3.1    0.2    0.1    0.5    2.6    1.0    0.3    0.2    1.8
    6.4    2.5    0.4    0.3    0.6    0.3    0.3    0.3   84.6    0.5    0.0    0.1    0.2    0.2    0.1    0.3    1.4    0.8    0.1    0.0    0.5
    5.9    0.2    4.9    3.0    1.0    0.8    2.7    2.3    2.1   60.3    0.0    2.3    0.3    1.0    0.9    1.7    4.4    3.6    0.6    1.6    0.7
    4.2    0.4    0.5    0.4    0.1    0.6    0.1    0.1    0.0    0.1   62.0    8.3    0.3    2.2    2.6    0.3    0.4    1.5    0.3    0.5   15.1
    8.1    0.8    0.2    0.2    0.1    0.5    0.7    0.3    0.3    0.6    4.4   72.2    0.3    2.8    2.3    0.5    0.3    0.3    0.2    0.8    4.2
    8.3    1.6    9.8    1.5    0.4    0.4    3.2    2.2    0.3    1.2    1.0    1.1   60.9    0.3    0.4    0.5    1.7    3.4    0.4    0.6    0.9
    7.3    4.4    1.9    0.4    0.2    0.8    2.7    1.0    1.0    0.2    4.4    7.5    1.4   56.2    2.4    0.5    1.9    2.5    0.1    0.1    3.2
    4.2    0.1    0.1    0.2    0.1    0.6    0.0    0.0    0.6    0.4    2.4    2.9    0.2    1.4   75.8    0.0    0.9    0.7    1.2    6.3    2.0
   16.8    3.6    0.2    0.3    0.3    0.0    1.1    0.3    1.1    0.4    0.1    0.8    0.4    0.1    0.0   69.9    3.1    1.2    0.0    0.1    0.1
   16.3    2.3    1.7    2.4    0.8    0.7    0.7    0.9    4.0    1.1    0.3    0.1    1.0    0.5    0.6    1.8   59.3    4.6    0.1    0.3    0.7
    7.7    2.9    1.3    1.4    1.4    0.4    0.7    2.6    0.6    0.9    2.1    1.0    3.4    0.6    0.2    0.3    5.2   64.0    0.2    0.7    2.7
    5.5    0.0    0.5    0.0    0.0    0.0    0.1    0.1    0.0    0.1    0.1    0.8    0.1    0.5    1.8    0.0    0.5    0.0   87.5    2.3    0.0
    4.4    0.5    0.8    1.2    0.1    0.9    0.5    0.2    0.0    1.9    1.3    1.2    0.6    0.0    6.1    0.4    1.2    0.6    0.7   77.2    0.3
    6.3    2.2    0.7    0.2    0.3    0.6    0.6    0.7    0.1    0.2    8.7    3.1    0.3    0.8    0.7    0.4    1.2    2.5    0.2    0.3   70.1
//
H KOSJ950111
D Context-dependent optimal substitution matrices for turn
  (Koshi-Goldstein, 1995)
R PMID:8577693
A Koshi, J.M. and Goldstein, R.A.
T Context-dependent optimal substitution matrices.
J Protein Engineering 8, 641-645 (1995)
M rows = -ARNDCQEGHILKMFPSTWYV, cols = -ARNDCQEGHILKMFPSTWYV
   74.2    3.1    1.1    1.3    0.6    1.7    2.1    1.0    1.0    1.2    1.5    1.0    0.4    1.5    1.5    0.7    1.1    1.3    1.0    1.7    1.2
   15.8   54.3    1.1    1.3    1.6    2.1    0.8    0.9    3.4    0.6    1.6    2.4    1.2    0.4    0.2    1.8    4.2    2.3    0.3    0.1    3.6
    5.5    1.1   68.1    2.3    1.3    0.3    2.8    0.2    1.7    1.9    0.4    0.5    6.9    0.4    0.3    0.7    2.5    1.1    0.5    0.5    1.1
    6.7    1.5    1.4   60.1    6.7    0.4    1.4    1.6    4.2    1.3    0.0    0.8    3.6    0.5    0.2    0.3    6.4    1.0    0.2    1.1    0.7
    3.2    1.9    0.3    7.5   64.1    0.6    1.5    8.3    3.3    0.6    0.1    0.2    2.4    0.0    0.0    1.3    2.9    1.2    0.0    0.3    0.4
    9.1    8.6    0.1    0.1    2.6   67.0    0.0    1.3    2.3    1.1    0.4    0.0    0.0    0.2    2.3    0.3    2.6    0.0    0.2    1.2    0.6
   10.9    3.2    3.5    2.1    1.8    0.0   52.5    4.0    1.6    2.5    1.4    3.9    4.7    0.9    0.2    2.3    0.7    2.2    0.4    0.0    1.4
    5.1    3.8    1.0    1.3    7.4    0.3    4.1   60.0    0.9    1.2    0.8    1.2    4.7    0.3    0.3    2.0    2.9    1.5    0.2    0.2    1.0
    5.1    2.7    0.4    2.2    2.1    0.6    0.6    1.5   78.5    0.3    0.0    0.2    1.5    0.1    0.3    0.2    1.9    1.5    0.1    0.1    0.2
    6.2    2.5    0.5    3.1    0.1    0.7    1.8    2.4    0.7   64.6    0.6    0.7    2.6    1.0    2.2    2.6    2.0    0.8    0.0    5.1    0.0
    7.6    0.4    0.1    0.2    0.0    0.4    0.3    0.4    0.0    0.1   68.5    6.5    0.3    3.1    1.1    0.4    0.1    2.2    0.1    0.5    7.7
    5.3    1.3    2.2    0.2    0.7    0.2    1.0    0.8    0.4    0.4    4.9   70.1    0.4    3.9    2.3    0.3    0.3    0.8    0.6    1.0    3.1
    2.3    3.8    8.2    2.7    1.2    0.0    5.4    3.6    1.4    1.3    0.1    1.5   60.8    0.6    0.5    0.4    2.8    2.1    0.0    0.4    1.1
    7.7    0.4    1.2    0.1    0.0    0.9    0.2    1.3    0.0    0.2    3.3    7.8    0.9   67.3    3.3    0.0    0.1    0.7    0.4    1.3    2.9
    7.8    0.0    0.6    0.9    0.0    0.6    0.7    0.1    0.1    0.8    0.6    3.1    0.6    0.9   73.1    0.4    0.5    0.0    1.8    5.7    1.8
    3.5    4.6    1.4    1.1    0.8    0.1    0.6    1.5    0.7    0.6    0.7    1.0    1.6    0.2    0.4   76.2    2.7    1.8    0.1    0.2    0.4
    6.0    8.2    1.5    2.7    4.2    1.1    1.8    1.6    4.5    0.8    0.3    1.2    2.6    0.3    0.6    1.2   52.9    6.9    0.3    0.8    0.7
    7.0    2.9    0.9    3.1    1.5    0.2    1.3    1.5    1.0    0.2    2.0    0.6    1.9    1.0    0.1    1.2   10.0   60.7    0.2    0.2    2.6
    5.2    0.1    0.1    0.0    0.0    0.9    0.1    0.0    0.4    0.0    0.5    0.1    0.0    1.5    1.3    0.3    1.1    0.7   82.1    4.9    0.7
    8.8    0.5    0.3    0.3    0.1    0.3    0.2    0.8    0.0    2.1    0.9    2.0    0.7    0.3    6.8    0.0    0.2    0.8    1.2   73.4    0.4
    6.4    3.9    0.3    0.7    0.2    0.8    0.8    0.2    0.8    0.1    8.4    4.8    0.7    0.7    2.2    0.8    0.7    2.8    0.5    1.5   62.8
//
H KOSJ950112
D Context-dependent optimal substitution matrices for coil
  (Koshi-Goldstein, 1995)
R PMID:8577693
A Koshi, J.M. and Goldstein, R.A.
T Context-dependent optimal substitution matrices.
J Protein Engineering 8, 641-645 (1995)
M rows = -ARNDCQEGHILKMFPSTWYV, cols = -ARNDCQEGHILKMFPSTWYV
   60.6    3.0    2.1    1.0    1.3    2.0    2.9    3.2    1.8    2.0    2.7    1.5    1.5    2.4    1.6    1.8    1.5    1.8    1.3    1.7    2.4
   19.0   55.6    0.4    0.5    0.8    2.7    1.2    0.8    4.3    0.3    0.6    0.8    0.8    0.2    0.3    2.3    4.7    2.6    0.0    0.1    2.0
   13.6    0.5   64.3    1.3    0.1    0.1    1.3    0.6    0.2    2.0    0.2    1.3    5.8    0.0    0.1    1.6    2.7    2.9    0.4    0.7    0.5
    6.4    1.0    1.9   59.8    4.8    0.7    1.6    2.8    2.3    2.2    0.7    0.9    3.6    0.8    0.2    0.1    5.4    2.6    0.1    1.0    1.3
    8.6    1.5    0.5    6.2   66.7    0.3    1.8    5.0    1.2    0.6    0.6    0.5    1.3    0.1    0.1    1.2    1.6    1.1    0.0    1.1    0.2
   13.0   11.3    0.4    0.2    1.1   59.3    0.0    1.6    0.9    0.1    2.3    0.1    0.0    1.5    1.0    0.0    2.9    1.0    0.9    0.6    2.0
   19.2    1.5    2.5    1.7    1.3    0.0   51.2    7.4    0.9    0.9    0.3    0.7    3.1    1.3    0.7    0.3    2.3    3.2    0.0    0.5    1.1
   20.4    3.3    1.0    0.7    3.4    0.4    2.9   60.6    1.2    0.8    0.2    0.5    1.2    0.1    0.0    0.4    1.3    0.7    0.0    0.3    0.6
   11.7    1.2    0.2    1.0    1.3    0.3    0.4    0.8   77.9    0.3    0.1    0.1    0.5    0.1    0.1    0.5    2.0    0.8    0.1    0.3    0.4
   12.9    1.4    1.2    1.9    2.3    0.6    1.4    0.5    0.3   68.2    0.9    0.8    0.3    0.2    1.3    0.7    2.1    0.1    0.4    2.6    0.0
   17.1    0.6    0.4    0.2    0.1    0.6    0.3    1.0    0.4    0.2   55.0    5.2    1.1    1.6    1.6    0.9    0.4    1.0    0.7    0.3   11.5
   10.2    0.8    0.6    0.2    0.1    0.3    1.5    0.2    0.3    0.6    4.9   68.2    0.7    3.0    3.0    0.9    0.1    0.7    0.2    0.8    2.7
    9.7    3.4    6.0    1.7    2.7    0.0    3.2    3.9    2.0    1.3    0.4    1.3   55.4    0.4    0.6    1.9    2.8    1.9    0.2    0.2    1.3
   15.4    0.0    0.0    0.2    0.4    0.4    0.3    0.6    0.0    0.8    6.5    9.4    0.1   56.8    0.6    0.1    0.5    3.0    0.2    0.1    4.5
   10.2    0.2    0.4    0.2    0.0    0.2    0.5    0.0    0.3    0.4    1.2    3.6    0.1    0.6   70.9    1.1    0.8    0.7    1.1    5.9    1.7
   11.9    5.1    0.8    0.5    0.3    0.0    1.4    1.7    0.8    0.4    0.3    0.8    0.5    0.4    0.3   69.9    2.7    0.5    0.0    0.5    1.4
    9.9    4.4    0.7    3.4    3.2    1.3    0.9    1.3    2.5    0.5    0.4    0.4    1.2    0.1    0.3    3.6   57.1    6.9    0.3    0.5    1.2
   11.7    3.2    0.7    2.7    0.8    0.5    1.6    0.5    1.0    0.6    1.7    0.9    1.2    0.8    0.2    2.0    7.5   58.8    0.0    0.6    3.3
    8.4    0.0    0.4    0.5    0.0    0.2    0.0    0.0    0.0    0.1    2.9    0.9    0.9    0.7    4.3    0.0    1.4    0.0   76.5    2.1    0.7
   10.9    0.3    0.3    0.3    0.3    0.1    0.1    0.1    0.6    0.9    0.1    0.7    0.7    0.5    8.4    0.1    0.1    0.4    0.9   73.3    0.9
   15.5    3.3    0.1    0.9    0.3    0.7    0.3    0.8    0.3    0.1    6.3    3.9    0.8    1.1    1.0    0.5    1.6    3.0    0.3    0.5   58.8
//
H KOSJ950113
D Context-dependent optimal substitution matrices for exposed residues
  (Koshi-Goldstein, 1995)
R PMID:8577693
A Koshi, J.M. and Goldstein, R.A.
T Context-dependent optimal substitution matrices.
J Protein Engineering 8, 641-645 (1995)
M rows = -ARNDCQEGHILKMFPSTWYV, cols = -ARNDCQEGHILKMFPSTWYV
   60.2    3.3    1.7    1.1    1.1    2.8    2.1    1.2    1.8    2.2    2.6    2.3    0.7    2.2    2.2    2.1    1.7    2.1    2.1    1.8    2.7
   21.5   51.3    0.7    0.6    1.1    1.0    1.2    1.2    3.0    0.4    1.2    2.1    1.2    0.7    0.2    2.1    4.2    2.8    0.3    0.2    3.2
   11.4    1.2   62.9    1.6    0.7    0.1    2.9    0.9    0.7    1.6    0.6    1.1    7.3    0.5    0.4    0.6    2.2    1.6    0.6    0.4    0.8
    7.5    1.8    1.5   52.6    6.4    0.4    2.3    2.7    2.8    1.7    0.4    1.0    4.8    0.8    0.4    0.1    7.9    2.7    0.3    1.2    0.9
    7.4    2.8    0.7    8.0   59.2    0.3    1.7    8.3    2.3    0.3    0.4    0.4    2.3    0.2    0.1    1.4    2.6    1.2    0.0    0.4    0.2
   18.1    4.2    0.0    0.3    1.3   64.7    0.0    0.9    1.1    0.5    1.1    1.0    0.0    1.5    2.2    0.0    1.7    0.9    0.0    0.1    0.3
   13.9    3.1    3.7    1.8    1.7    0.1   51.0    5.9    1.0    1.7    0.5    3.0    3.9    0.8    0.1    1.0    2.3    2.6    0.1    0.6    1.4
    7.8    4.3    0.9    1.3    6.7    0.2    4.5   58.3    1.1    1.1    0.6    1.0    4.2    0.5    0.3    1.4    2.5    1.8    0.2    0.1    1.3
   11.8    2.6    0.4    2.2    2.3    0.3    0.6    1.6   71.0    0.3    0.0    0.1    1.2    0.3    0.5    0.3    2.2    1.7    0.2    0.2    0.4
   14.1    0.9    3.3    5.0    1.0    0.1    2.2    1.7    0.8   54.8    0.6    1.1    1.3    0.5    1.9    1.4    2.6    0.1    0.0    4.4    2.4
   17.2    0.3    0.3    0.2    0.1    0.3    0.2    0.3    0.0    0.1   54.4    7.6    0.7    2.0    1.5    0.6    0.0    2.1    0.3    0.6   11.3
   15.0    0.7    1.2    0.4    0.1    0.2    0.8    0.4    0.3    0.6    3.8   64.4    0.8    3.5    2.8    0.5    0.3    0.6    0.5    0.7    2.6
    4.8    3.8    7.9    2.3    1.6    0.2    4.6    4.9    1.2    1.3    0.4    1.4   56.0    0.4    0.4    0.9    3.0    3.2    0.1    0.3    1.4
   14.4    2.8    0.7    0.2    0.0    0.4    1.1    1.9    1.1    0.1    6.6    7.7    1.8   49.9    2.1    0.1    1.4    2.7    0.8    0.8    3.5
   14.2    0.6    0.5    0.5    0.2    0.5    0.4    0.2    0.1    0.5    1.7    2.8    0.7    0.6   66.6    0.4    0.8    0.5    1.1    5.9    1.2
   13.8    4.9    1.3    0.6    0.8    0.0    0.8    1.3    0.9    0.4    0.4    1.0    1.3    0.3    0.1   66.0    3.5    1.3    0.1    0.4    0.9
   11.3    7.4    1.3    2.7    3.0    0.9    1.1    1.9    4.3    0.8    0.1    0.5    1.8    0.3    0.3    2.3   50.1    8.1    0.0    0.5    1.3
   13.7    4.0    0.9    2.5    1.2    0.2    1.3    1.2    0.6    0.6    2.8    2.3    2.0    0.7    0.2    1.3    7.4   53.0    0.3    0.4    3.6
   13.7    0.1    0.1    0.1    0.0    0.0    0.0    0.0    0.0    0.0    0.6    2.0    0.5    0.2    2.5    0.4    0.0    0.1   75.4    4.2    0.1
   11.6    0.6    0.4    0.4    0.2    0.5    0.1    0.6    0.2    1.5    1.6    3.0    0.6    0.4    7.8    0.1    0.7    0.7    1.0   66.8    1.2
   17.5    2.5    0.4    0.5    0.4    0.6    0.8    0.6    0.6    0.6   10.4    3.7    0.7    0.9    1.6    0.3    0.7    1.6    0.3    0.7   54.8
//
H KOSJ950114
D Context-dependent optimal substitution matrices for buried residues
  (Koshi-Goldstein, 1995)
R PMID:8577693
A Koshi, J.M. and Goldstein, R.A.
T Context-dependent optimal substitution matrices.
J Protein Engineering 8, 641-645 (1995)
M rows = -ARNDCQEGHILKMFPSTWYV, cols = -ARNDCQEGHILKMFPSTWYV
   79.2    0.2    1.6    1.2    1.9    1.2    1.2    2.0    0.7    0.2    0.4    0.2    4.0    0.4    0.4    1.6    1.8    0.7    0.4    0.4    0.3
    1.0   76.3    0.6    0.5    0.6    1.7    0.6    1.0    2.8    0.2    0.9    1.5    0.4    0.5    0.3    1.1    4.4    1.7    0.0    0.4    3.7
    8.2    0.7   72.9    0.9    0.1    0.4    2.4    0.4    0.9    1.7    1.1    1.4    3.7    0.2    0.3    0.6    1.7    1.9    0.1    0.4    0.1
    6.2    2.0    1.1   65.7    3.1    0.6    1.3    0.9    2.5    1.6    1.2    1.5    1.6    0.4    0.1    0.5    4.8    2.6    0.1    1.0    1.3
    9.7    2.5    0.6    3.0   66.9    0.4    0.6    4.2    2.0    0.7    0.8    0.8    0.9    0.0    0.2    1.0    2.7    1.5    0.2    1.0    0.5
    5.7    6.9    0.1    0.1    1.5   71.6    0.1    0.6    1.4    0.3    1.8    2.0    0.0    0.5    1.3    0.0    2.0    0.7    0.1    0.1    3.2
    6.1    2.4    1.7    1.3    0.9    0.4   67.3    2.0    0.8    1.9    0.6    3.6    2.9    2.3    1.0    0.9    1.3    1.1    0.8    0.4    0.5
    9.9    4.0    1.8    0.6    2.5    0.4    3.8   62.5    1.8    0.5    0.1    2.5    1.6    0.3    0.0    0.5    2.5    1.0    0.0    1.3    2.5
    3.6    3.6    0.3    0.6    0.5    0.3    0.4    0.4   85.7    0.2    0.1    0.3    0.5    0.1    0.1    0.2    1.7    0.7    0.2    0.1    0.4
    1.0    0.6    0.8    0.9    0.6    0.4    1.4    0.5    0.0   84.1    0.6    1.0    0.6    0.8    2.0    0.3    0.5    0.5    0.6    2.6    0.2
    1.8    0.4    0.3    0.3    0.2    0.4    0.1    0.2    0.0    0.1   73.9    7.7    0.4    2.2    1.5    0.2    0.3    0.8    0.2    0.2    8.8
    1.1    0.6    0.3    0.4    0.2    0.5    0.9    0.6    0.2    0.2    5.0   78.6    1.1    3.0    2.4    0.3    0.1    0.4    0.2    0.5    3.4
   20.3    1.8    5.4    1.6    0.5    0.0    1.3    1.8    1.7    1.5    1.6    4.8   46.8    1.1    0.6    0.4    1.1    2.8    0.2    1.1    3.7
    2.2    1.2    0.2    0.3    0.2    0.7    0.6    0.3    0.4    0.2    5.1   12.2    0.3   68.7    2.2    0.1    0.1    0.4    0.4    0.1    4.2
    1.9    0.2    0.1    0.1    0.1    0.3    0.2    0.0    0.4    0.5    1.5    4.7    0.1    1.0   80.2    0.1    0.5    0.4    1.6    4.6    1.4
    7.8    4.6    0.4    1.0    0.2    0.1    1.2    0.8    0.9    0.8    1.0    1.3    0.3    0.5    0.4   73.3    2.9    1.5    0.0    0.0    1.0
    8.8    7.1    1.1    1.5    0.8    1.6    0.9    0.6    2.2    0.8    0.5    0.4    0.7    0.4    1.1    1.2   62.2    5.9    0.1    0.9    1.2
    3.5    3.8    0.5    0.8    0.4    0.9    0.8    0.9    0.6    0.3    3.1    1.7    0.9    1.7    0.2    0.6    4.5   68.2    0.0    0.4    6.4
    1.9    0.0    0.6    0.0    0.0    0.4    0.2    0.0    0.2    0.1    0.7    0.8    0.7    0.7    1.4    0.0    0.5    0.2   89.0    1.7    0.8
    2.0    0.4    0.4    0.6    0.2    0.6    0.2    0.3    0.0    1.5    0.9    2.0    0.5    0.5    9.7    0.2    0.2    0.5    0.7   78.0    0.6
    1.4    2.5    0.2    0.3    0.2    0.8    0.1    0.6    0.1    0.1   11.1    3.8    0.9    1.0    1.2    0.3    0.5    1.6    0.2    0.1   73.0
//
H KOSJ950115
D Context-dependent optimal substitution matrices for all residues
  (Koshi-Goldstein, 1995)
R PMID:8577693
A Koshi, J.M. and Goldstein, R.A.
T Context-dependent optimal substitution matrices.
J Protein Engineering 8, 641-645 (1995)
M rows = -ARNDCQEGHILKMFPSTWYV, cols = -ARNDCQEGHILKMFPSTWYV
   69.2    1.6    2.0    1.1    1.3    2.4    2.0    1.4    1.5    1.7    1.2    1.3    0.9    1.7    1.1    2.1    2.1    1.5    1.0    1.3    1.7
    8.9   61.9    0.8    0.6    1.3    1.6    1.0    1.6    3.7    0.3    0.6    1.6    1.3    0.5    0.2    1.9    5.9    3.2    0.2    0.4    2.6
   11.3    1.3   67.2    1.4    0.7    0.2    2.4    0.7    0.6    1.3    0.6    1.0    5.7    0.3    0.2    0.7    1.9    1.4    0.3    0.5    0.4
    6.4    1.8    1.5   60.9    5.4    0.3    1.8    2.0    2.5    1.6    0.5    0.8    3.5    0.7    0.1    0.4    5.6    2.0    0.4    1.0    1.0
    7.3    2.0    0.5    6.1   65.0    0.4    1.2    6.9    1.9    0.3    0.4    0.4    1.9    0.3    0.2    1.1    2.4    1.0    0.0    0.5    0.2
   13.8    6.6    0.0    0.3    1.6   64.4    0.0    1.2    1.3    0.5    1.8    1.2    0.0    0.5    1.6    0.0    2.6    1.0    0.2    0.2    1.2
   11.4    2.4    3.3    1.6    1.7    0.2   58.4    4.9    1.0    1.8    0.5    2.0    3.5    0.8    0.3    1.0    1.9    1.9    0.5    0.5    0.6
    7.9    3.2    1.0    1.4    5.8    0.3    4.3   62.1    1.2    0.9    0.4    1.1    4.0    0.2    0.1    1.2    2.2    1.3    0.2    0.1    1.2
    8.4    2.5    0.4    1.4    1.6    0.4    0.5    1.1   77.8    0.3    0.0    0.2    1.0    0.1    0.2    0.3    1.9    1.1    0.1    0.2    0.4
    9.5    0.9    2.7    2.8    1.1    0.3    2.4    1.4    0.8   65.4    0.5    1.5    1.5    0.8    1.5    1.0    1.9    0.5    0.4    2.9    0.3
    6.9    0.8    0.3    0.4    0.1    0.4    0.1    0.4    0.2    0.1   64.8    7.7    0.4    2.0    1.7    0.3    0.3    1.6    0.3    0.3   10.9
    7.1    0.9    0.7    0.2    0.1    0.3    1.0    0.3    0.1    0.4    4.7   71.7    0.8    3.2    2.8    0.3    0.2    0.6    0.2    0.8    3.7
    5.0    2.9    8.1    2.3    1.4    0.1    4.1    4.3    1.1    1.2    0.4    1.4   58.7    0.5    0.5    1.2    2.5    2.6    0.1    0.3    1.4
    9.4    2.0    0.8    0.2    1.3    0.4    1.0    0.9    0.6    0.2    5.5    9.2    0.8   59.4    2.2    0.1    0.6    1.7    0.2    0.2    3.4
    6.4    0.3    0.2    0.4    0.2    0.4    0.4    0.2    0.3    0.4    1.4    3.7    0.1    0.9   73.8    0.3    0.9    0.6    1.4    6.4    1.5
   12.0    3.5    0.9    0.6    0.6    0.0    0.8    1.0    0.7    0.4    0.5    0.9    0.9    0.6    0.1   71.2    2.8    1.4    0.0    0.5    0.7
   11.7    5.1    1.4    3.0    2.2    0.9    1.1    1.5    3.3    0.6    0.4    0.5    1.4    0.3    0.5    1.8   56.8    6.1    0.3    0.5    0.8
    8.8    3.1    0.9    2.2    1.1    0.4    1.1    1.2    0.9    0.6    2.0    1.4    2.0    0.8    0.1    1.1    6.9   61.8    0.1    0.4    3.2
    6.0    0.1    0.4    0.1    0.0    0.7    0.1    0.0    0.5    0.1    0.4    1.0    0.6    0.8    2.3    0.0    1.3    0.2   82.3    2.5    0.7
    7.4    0.6    0.5    0.6    0.4    0.7    0.2    0.5    0.3    1.7    0.9    2.0    0.6    0.4    7.1    0.1    0.6    0.9    0.7   73.2    0.7
    9.8    3.7    0.5    0.4    0.2    0.8    0.5    0.4    0.3    0.1    8.8    3.6    0.4    0.8    1.2    0.4    0.9    2.5    0.2    0.5   64.0
//
H OVEJ920102
D Environment-specific amino acid substitution matrix for alpha residues
  (Overington et al., 1992)
R PMID:1304904
A Overington, J., Donnelly, D., Johnson, M.S., Sali, A. and Blundell, T.L.
T Environment-specific amino acid substitution tables: tertiary templates
  and prediction of protein folds
J Protein Science 1, 216-226 (1992)
M rows = ACDEFGHIKLMNPQRSTVWYJ-, cols = ACDEFGHIKLMNPQRSTVWYJ
   0.355   0.007   0.090   0.100   0.050   0.177   0.037   0.077   0.096   0.056   0.081   0.103   0.106   0.090   0.088   0.163   0.120   0.098   0.065   0.036   0.252
   0.001   0.901   0.000   0.000   0.000   0.000   0.000   0.004   0.001   0.000   0.000   0.003   0.000   0.006   0.006   0.004   0.002   0.000   0.007   0.000   0.000
   0.038   0.000   0.315   0.109   0.006   0.041   0.027   0.009   0.033   0.004   0.009   0.088   0.051   0.089   0.023   0.065   0.048   0.013   0.012   0.011   0.009
   0.044   0.011   0.111   0.305   0.011   0.048   0.026   0.011   0.059   0.013   0.009   0.068   0.069   0.086   0.053   0.033   0.045   0.017   0.012   0.018   0.000
   0.017   0.000   0.005   0.007   0.415   0.004   0.009   0.039   0.025   0.097   0.042   0.013   0.006   0.011   0.009   0.009   0.014   0.041   0.053   0.085   0.009
   0.065   0.000   0.070   0.042   0.006   0.370   0.017   0.022   0.029   0.013   0.015   0.036   0.043   0.031   0.013   0.068   0.049   0.014   0.009   0.021   0.045
   0.010   0.000   0.012   0.011   0.010   0.007   0.571   0.003   0.022   0.005   0.015   0.043   0.006   0.035   0.021   0.016   0.008   0.017   0.009   0.037   0.009
   0.029   0.014   0.009   0.008   0.048   0.021   0.004   0.325   0.017   0.076   0.107   0.018   0.007   0.007   0.015   0.014   0.033   0.112   0.016   0.030   0.018
   0.053   0.007   0.044   0.081   0.020   0.041   0.044   0.026   0.336   0.029   0.059   0.073   0.045   0.094   0.163   0.041   0.054   0.026   0.041   0.028   0.036
   0.038   0.000   0.006   0.018   0.210   0.019   0.004   0.139   0.033   0.415   0.225   0.033   0.016   0.041   0.028   0.029   0.026   0.133   0.037   0.057   0.036
   0.013   0.000   0.004   0.003   0.016   0.007   0.000   0.043   0.014   0.053   0.197   0.010   0.000   0.018   0.004   0.003   0.010   0.018   0.021   0.021   0.018
   0.031   0.007   0.057   0.035   0.010   0.026   0.054   0.012   0.034   0.012   0.013   0.195   0.015   0.066   0.026   0.037   0.046   0.012   0.002   0.048   0.000
   0.022   0.000   0.036   0.035   0.005   0.026   0.011   0.009   0.020   0.006   0.000   0.013   0.424   0.013   0.016   0.039   0.011   0.009   0.002   0.000   0.000
   0.025   0.011   0.045   0.039   0.011   0.021   0.031   0.004   0.045   0.015   0.035   0.059   0.015   0.183   0.029   0.030   0.030   0.008   0.007   0.025   0.009
   0.019   0.011   0.012   0.023   0.005   0.008   0.019   0.010   0.069   0.009   0.004   0.018   0.013   0.028   0.348   0.030   0.019   0.005   0.007   0.018   0.018
   0.086   0.021   0.075   0.047   0.012   0.079   0.033   0.020   0.041   0.020   0.009   0.089   0.082   0.069   0.063   0.264   0.096   0.028   0.005   0.020   0.054
   0.043   0.007   0.039   0.033   0.020   0.038   0.014   0.026   0.032   0.015   0.026   0.057   0.028   0.046   0.035   0.065   0.266   0.037   0.016   0.034   0.000
   0.055   0.000   0.018   0.021   0.069   0.022   0.044   0.178   0.025   0.111   0.016   0.018   0.025   0.017   0.015   0.129   0.060   0.350   0.012   0.043   0.162
   0.009   0.000   0.003   0.004   0.022   0.004   0.007   0.006   0.012   0.006   0.020   0.001   0.001   0.006   0.004   0.002   0.007   0.003   0.588   0.064   0.000
   0.009   0.000   0.006   0.006   0.046   0.006   0.029   0.014   0.007   0.013   0.031   0.033   0.003   0.020   0.010   0.007   0.017   0.016   0.078   0.377   0.027
   0.009   0.000   0.001   0.000   0.001   0.004   0.001   0.002   0.002   0.002   0.004   0.000   0.000   0.004   0.003   0.006   0.004   0.010   0.000   0.005   0.297
   0.028   0.004   0.041   0.074   0.010   0.029   0.017   0.022   0.050   0.031   0.033   0.031   0.045   0.039   0.028   0.047   0.034   0.032   0.002   0.021   0.000
//
H OVEJ920103
D Environment-specific amino acid substitution matrix for beta residues
  (Overington et al., 1992)
R PMID:1304904
A Overington, J., Donnelly, D., Johnson, M.S., Sali, A. and Blundell, T.L.
T Environment-specific amino acid substitution tables: tertiary templates
  and prediction of protein folds
J Protein Science 1, 216-226 (1992)
M rows = ACDEFGHIKLMNPQRSTVWYJ-, cols = ACDEFGHIKLMNPQRSTVWYJ
   0.275   0.000   0.025   0.047   0.023   0.086   0.007   0.029   0.036   0.031   0.074   0.041   0.035   0.050   0.050   0.057   0.055   0.065   0.014   0.031   0.080
   0.000   0.910   0.000   0.016   0.014   0.000   0.000   0.003   0.008   0.000   0.000   0.000   0.000   0.008   0.015   0.002   0.001   0.000   0.000   0.000   0.020
   0.008   0.000   0.350   0.059   0.008   0.011   0.014   0.017   0.018   0.006   0.000   0.095   0.040   0.020   0.010   0.026   0.020   0.013   0.006   0.012   0.000
   0.018   0.016   0.054   0.192   0.004   0.015   0.021   0.012   0.071   0.009   0.037   0.039   0.028   0.056   0.053   0.018   0.036   0.018   0.002   0.015   0.000
   0.020   0.022   0.013   0.005   0.398   0.008   0.021   0.049   0.017   0.046   0.023   0.006   0.012   0.006   0.015   0.020   0.012   0.021   0.071   0.096   0.020
   0.092   0.000   0.021   0.033   0.015   0.623   0.007   0.016   0.018   0.016   0.042   0.019   0.017   0.033   0.017   0.036   0.028   0.013   0.049   0.021   0.020
   0.003   0.000   0.006   0.010   0.008   0.002   0.332   0.006   0.022   0.004   0.000   0.035   0.014   0.021   0.023   0.009   0.010   0.009   0.000   0.008   0.020
   0.040   0.010   0.044   0.021   0.089   0.020   0.017   0.358   0.022   0.105   0.077   0.025   0.012   0.010   0.015   0.021   0.026   0.119   0.041   0.034   0.020
   0.024   0.011   0.021   0.099   0.015   0.007   0.070   0.013   0.299   0.017   0.012   0.060   0.052   0.060   0.139   0.026   0.051   0.010   0.004   0.017   0.040
   0.057   0.000   0.027   0.031   0.111   0.023   0.031   0.143   0.051   0.459   0.169   0.031   0.038   0.026   0.031   0.025   0.028   0.119   0.096   0.044   0.060
   0.026   0.000   0.006   0.021   0.011   0.013   0.021   0.021   0.007   0.031   0.244   0.010   0.002   0.031   0.002   0.007   0.013   0.019   0.006   0.006   0.000
   0.016   0.000   0.092   0.044   0.003   0.018   0.073   0.008   0.038   0.008   0.019   0.261   0.026   0.016   0.011   0.036   0.032   0.004   0.012   0.017   0.000
   0.014   0.000   0.027   0.020   0.001   0.005   0.021   0.007   0.029   0.019   0.002   0.017   0.504   0.011   0.023   0.010   0.021   0.009   0.018   0.003   0.000
   0.038   0.014   0.033   0.068   0.006   0.020   0.073   0.008   0.071   0.014   0.077   0.037   0.019   0.414   0.118   0.025   0.045   0.015   0.002   0.013   0.000
   0.022   0.011   0.006   0.042   0.007   0.010   0.038   0.008   0.079   0.008   0.002   0.012   0.031   0.055   0.214   0.015   0.027   0.010   0.014   0.017   0.000
   0.078   0.003   0.085   0.041   0.029   0.056   0.052   0.024   0.048   0.022   0.030   0.112   0.040   0.042   0.065   0.403   0.140   0.028   0.014   0.040   0.040
   0.081   0.002   0.075   0.111   0.021   0.037   0.052   0.027   0.095   0.022   0.049   0.110   0.073   0.078   0.092   0.153   0.363   0.044   0.008   0.037   0.020
   0.141   0.000   0.058   0.065   0.074   0.027   0.070   0.202   0.034   0.145   0.123   0.019   0.033   0.039   0.046   0.043   0.062   0.446   0.027   0.059   0.040
   0.005   0.000   0.008   0.002   0.048   0.000   0.000   0.013   0.001   0.019   0.005   0.015   0.012   0.001   0.013   0.003   0.002   0.005   0.559   0.017   0.000
   0.026   0.000   0.027   0.037   0.112   0.011   0.049   0.024   0.020   0.018   0.014   0.033   0.005   0.013   0.032   0.026   0.022   0.023   0.051   0.505   0.000
   0.003   0.002   0.000   0.000   0.001   0.001   0.007   0.001   0.003   0.001   0.000   0.000   0.000   0.000   0.000   0.002   0.001   0.001   0.000   0.000   0.620
   0.012   0.000   0.021   0.007   0.002   0.006   0.021   0.012   0.013   0.004   0.002   0.021   0.007   0.008   0.015   0.038   0.007   0.009   0.004   0.009   0.000
//
H OVEJ920104
D Environment-specific amino acid substitution matrix for accessible
  residues (Overington et al., 1992)
R PMID:1304904
A Overington, J., Donnelly, D., Johnson, M.S., Sali, A. and Blundell, T.L.
T Environment-specific amino acid substitution tables: tertiary templates
  and prediction of protein folds
J Protein Science 1, 216-226 (1992)
M rows = ACDEFGHIKLMNPQRSTVWYJ-, cols = ACDEFGHIKLMNPQRSTVWYJ
   0.224   0.013   0.055   0.068   0.031   0.067   0.048   0.053   0.068   0.050   0.087   0.059   0.067   0.073   0.062   0.074   0.059   0.079   0.033   0.035   0.121
   0.002   0.739   0.001   0.006   0.012   0.000   0.001   0.004   0.003   0.000   0.000   0.001   0.001   0.005   0.008   0.001   0.001   0.000   0.001   0.000   0.008
   0.044   0.007   0.284   0.091   0.016   0.041   0.056   0.033   0.034   0.012   0.022   0.094   0.047   0.052   0.025   0.054   0.044   0.025   0.014   0.023   0.030
   0.052   0.029   0.079   0.251   0.016   0.028   0.026   0.026   0.053   0.019   0.031   0.038   0.037   0.071   0.049   0.031   0.044   0.034   0.010   0.027   0.008
   0.010   0.029   0.006   0.008   0.291   0.004   0.023   0.046   0.011   0.047   0.032   0.012   0.006   0.010   0.009   0.011   0.013   0.018   0.093   0.073   0.000
   0.079   0.000   0.066   0.047   0.020   0.455   0.042   0.024   0.033   0.028   0.039   0.073   0.054   0.054   0.040   0.064   0.037   0.039   0.041   0.036   0.038
   0.013   0.003   0.021   0.011   0.024   0.010   0.284   0.008   0.021   0.011   0.020   0.035   0.008   0.020   0.023   0.013   0.012   0.020   0.014   0.025   0.023
   0.014   0.016   0.017   0.014   0.058   0.006   0.010   0.235   0.015   0.050   0.048   0.018   0.009   0.009   0.015   0.014   0.023   0.075   0.015   0.030   0.008
   0.062   0.007   0.039   0.072   0.032   0.027   0.068   0.039   0.294   0.050   0.077   0.055   0.045   0.077   0.122   0.043   0.059   0.044   0.037   0.035   0.053
   0.028   0.000   0.010   0.017   0.097   0.013   0.024   0.094   0.035   0.311   0.141   0.030   0.030   0.028   0.027   0.019   0.029   0.073   0.064   0.033   0.015
   0.010   0.000   0.003   0.005   0.015   0.005   0.005   0.020   0.011   0.030   0.167   0.004   0.003   0.017   0.005   0.003   0.007   0.013   0.004   0.008   0.015
   0.041   0.007   0.080   0.041   0.022   0.044   0.087   0.031   0.042   0.035   0.024   0.239   0.019   0.040   0.031   0.050   0.051   0.021   0.008   0.036   0.030
   0.053   0.000   0.039   0.036   0.036   0.006   0.027   0.018   0.017   0.034   0.014   0.018   0.412   0.021   0.026   0.037   0.031   0.019   0.018   0.008   0.015
   0.040   0.013   0.038   0.060   0.018   0.025   0.042   0.017   0.046   0.026   0.075   0.032   0.019   0.231   0.056   0.032   0.042   0.036   0.007   0.015   0.023
   0.025   0.023   0.015   0.031   0.010   0.017   0.033   0.017   0.062   0.019   0.015   0.022   0.018   0.047   0.248   0.026   0.028   0.022   0.022   0.023   0.000
   0.100   0.013   0.088   0.059   0.044   0.073   0.057   0.051   0.062   0.043   0.026   0.096   0.070   0.072   0.079   0.290   0.138   0.057   0.025   0.059   0.053
   0.054   0.010   0.049   0.058   0.042   0.029   0.037   0.059   0.058   0.039   0.049   0.068   0.042   0.066   0.053   0.099   0.266   0.061   0.021   0.041   0.015
   0.041   0.000   0.021   0.033   0.040   0.020   0.038   0.148   0.031   0.077   0.051   0.018   0.020   0.043   0.033   0.028   0.044   0.269   0.023   0.049   0.091
   0.005   0.000   0.002   0.002   0.049   0.006   0.006   0.009   0.006   0.017   0.005   0.003   0.004   0.003   0.008   0.003   0.004   0.003   0.421   0.038   0.000
   0.014   0.000   0.013   0.018   0.111   0.012   0.034   0.028   0.017   0.023   0.026   0.023   0.005   0.012   0.024   0.018   0.019   0.028   0.109   0.355   0.023
   0.002   0.000   0.001   0.000   0.001   0.002   0.002   0.001   0.002   0.001   0.003   0.001   0.001   0.001   0.001   0.002   0.001   0.007   0.000   0.001   0.341
   0.086   0.092   0.072   0.072   0.045   0.089   0.060   0.043   0.061   0.075   0.048   0.061   0.083   0.050   0.056   0.087   0.050   0.057   0.021   0.048   0.091
//
H OVEJ920105
D Environment-specific amino acid substitution matrix for inaccessible residues
  (Overington et al., 1992)
R PMID:1304904
A Overington, J., Donnelly, D., Johnson, M.S., Sali, A. and Blundell, T.L.
T Environment-specific amino acid substitution tables: tertiary templates
  and prediction of protein folds
J Protein Science 1, 216-226 (1992)
M rows = ACDEFGHIKLMNPQRSTVWYJ-, cols = ACDEFGHIKLMNPQRSTVWYJ
   0.426   0.022   0.025   0.095   0.036   0.075   0.009   0.039   0.000   0.029   0.061   0.036   0.041   0.053   0.015   0.149   0.103   0.071   0.020   0.032   0.112
   0.007   0.879   0.000   0.000   0.005   0.000   0.000   0.003   0.000   0.001   0.000   0.000   0.000   0.000   0.000   0.008   0.004   0.000   0.003   0.001   0.004
   0.012   0.000   0.775   0.042   0.002   0.008   0.004   0.007   0.000   0.002   0.001   0.112   0.004   0.011   0.000   0.016   0.005   0.005   0.000   0.006   0.000
   0.007   0.009   0.011   0.460   0.004   0.008   0.000   0.005   0.000   0.003   0.009   0.036   0.000   0.064   0.015   0.009   0.001   0.006   0.000   0.001   0.000
   0.022   0.014   0.004   0.011   0.493   0.006   0.015   0.045   0.000   0.075   0.036   0.006   0.016   0.005   0.000   0.012   0.013   0.033   0.058   0.143   0.017
   0.070   0.000   0.016   0.037   0.006   0.732   0.000   0.013   0.000   0.007   0.015   0.009   0.004   0.013   0.023   0.064   0.032   0.008   0.005   0.004   0.043
   0.005   0.000   0.002   0.000   0.003   0.003   0.705   0.003   0.029   0.003   0.006   0.058   0.000   0.061   0.008   0.008   0.001   0.006   0.005   0.014   0.000
   0.043   0.007   0.009   0.032   0.061   0.017   0.009   0.402   0.029   0.110   0.096   0.015   0.018   0.008   0.008   0.013   0.036   0.135   0.043   0.038   0.017
   0.014   0.010   0.000   0.005   0.002   0.004   0.002   0.003   0.412   0.003   0.004   0.021   0.014   0.008   0.145   0.013   0.007   0.004   0.000   0.006   0.004
   0.048   0.005   0.005   0.037   0.162   0.015   0.022   0.163   0.015   0.524   0.250   0.033   0.031   0.032   0.038   0.027   0.022   0.130   0.048   0.052   0.030
   0.019   0.000   0.004   0.037   0.014   0.004   0.019   0.027   0.000   0.048   0.262   0.027   0.000   0.072   0.000   0.009   0.018   0.020   0.014   0.017   0.009
   0.011   0.000   0.071   0.011   0.005   0.007   0.028   0.006   0.000   0.002   0.013   0.398   0.007   0.005   0.008   0.035   0.012   0.003   0.006   0.009   0.009
   0.014   0.002   0.005   0.000   0.011   0.013   0.004   0.005   0.000   0.002   0.000   0.015   0.764   0.008   0.008   0.005   0.012   0.007   0.000   0.001   0.000
   0.017   0.009   0.002   0.101   0.002   0.009   0.039   0.001   0.088   0.003   0.039   0.018   0.000   0.560   0.122   0.008   0.001   0.007   0.006   0.005   0.004
   0.013   0.009   0.000   0.058   0.003   0.004   0.015   0.004   0.294   0.003   0.001   0.000   0.002   0.040   0.588   0.013   0.002   0.004   0.003   0.007   0.009
   0.074   0.010   0.023   0.016   0.011   0.039   0.017   0.009   0.015   0.007   0.016   0.103   0.020   0.013   0.000   0.450   0.111   0.017   0.005   0.004   0.052
   0.044   0.006   0.012   0.000   0.006   0.018   0.006   0.015   0.015   0.009   0.025   0.024   0.025   0.005   0.008   0.081   0.504   0.025   0.002   0.005   0.034
   0.116   0.001   0.012   0.053   0.073   0.015   0.054   0.205   0.000   0.134   0.118   0.033   0.031   0.027   0.015   0.043   0.079   0.476   0.014   0.047   0.082
   0.006   0.003   0.007   0.000   0.024   0.001   0.011   0.011   0.000   0.009   0.013   0.003   0.000   0.005   0.000   0.003   0.001   0.005   0.731   0.031   0.000
   0.015   0.001   0.005   0.000   0.071   0.006   0.034   0.021   0.029   0.013   0.023   0.024   0.007   0.008   0.000   0.014   0.012   0.017   0.037   0.561   0.009
   0.013   0.002   0.000   0.000   0.002   0.002   0.000   0.002   0.000   0.002   0.003   0.006   0.000   0.003   0.000   0.008   0.007   0.003   0.000   0.004   0.547
   0.006   0.010   0.012   0.005   0.007   0.013   0.006   0.011   0.074   0.010   0.009   0.018   0.016   0.000   0.000   0.011   0.018   0.016   0.002   0.012   0.017
//
H LINK010101
D Substitution matrices from an neural network model (Lin et al., 2001)
R PMID:11694178
A Lin, K., May, A.C. and Taylor, W.R.
T Amino acid substitution matrices from an artificial neural network 
  model
J J Comput Biol. 8, 471-481 (2001)
M rows = ARNDCQEGHILKMFPSTWYV, cols = ARNDCQEGHILKMFPSTWYV
   0.441   0.030   0.020   0.033   0.000   0.029   0.045   0.064   0.011   0.021   0.043   0.032   0.010   0.015   0.029   0.069   0.041   0.003   0.009   0.055
   0.034   0.519   0.026   0.012   0.001   0.047   0.033   0.022   0.014   0.020   0.029   0.134   0.007   0.005   0.019   0.041   0.013   0.004   0.015   0.004
   0.029   0.036   0.396   0.097   0.001   0.034   0.046   0.051   0.015   0.014   0.021   0.053   0.006   0.008   0.009   0.088   0.054   0.002   0.017   0.025
   0.039   0.012   0.070   0.522   0.000   0.031   0.102   0.042   0.008   0.003   0.006   0.036   0.002   0.007   0.014   0.047   0.031   0.002   0.011   0.016
   0.035   0.012   0.007   0.006   0.757   0.007   0.003   0.012   0.007   0.021   0.031   0.008   0.003   0.009   0.004   0.023   0.023   0.001   0.015   0.019
   0.055   0.061   0.031   0.043   0.001   0.395   0.121   0.022   0.022   0.014   0.011   0.092   0.013   0.005   0.013   0.036   0.044   0.004   0.006   0.014
   0.056   0.029   0.026   0.091   0.000   0.072   0.474   0.021   0.010   0.009   0.015   0.065   0.008   0.004   0.018   0.029   0.036   0.000   0.016   0.021
   0.060   0.023   0.027   0.036   0.001   0.016   0.007   0.691   0.008   0.007   0.017   0.022   0.000   0.001   0.017   0.038   0.015   0.000   0.002   0.012
   0.019   0.038   0.041   0.039   0.000   0.044   0.040   0.012   0.572   0.005   0.036   0.044   0.006   0.014   0.011   0.006   0.011   0.001   0.047   0.015
   0.024   0.011   0.006   0.003   0.000   0.009   0.010   0.011   0.003   0.464   0.157   0.015   0.028   0.016   0.011   0.008   0.039   0.001   0.009   0.175
   0.027   0.011   0.011   0.003   0.007   0.002   0.008   0.006   0.004   0.096   0.603   0.011   0.042   0.039   0.013   0.010   0.017   0.002   0.011   0.077
   0.050   0.107   0.034   0.039   0.001   0.057   0.070   0.019   0.013   0.018   0.019   0.411   0.004   0.008   0.022   0.044   0.057   0.002   0.010   0.019
   0.020   0.019   0.013   0.005   0.000   0.005   0.023   0.020   0.012   0.092   0.243   0.031   0.337   0.037   0.016   0.017   0.023   0.001   0.014   0.073
   0.027   0.005   0.004   0.010   0.003   0.003   0.001   0.010   0.011   0.009   0.088   0.011   0.015   0.605   0.009   0.014   0.023   0.017   0.111   0.024
   0.056   0.016   0.004   0.025   0.000   0.013   0.038   0.020   0.010   0.009   0.009   0.024   0.004   0.009   0.688   0.043   0.003   0.000   0.004   0.024
   0.104   0.030   0.052   0.033   0.001   0.027   0.043   0.039   0.004   0.020   0.015   0.032   0.004   0.012   0.027   0.408   0.111   0.002   0.017   0.022
   0.065   0.016   0.036   0.028   0.000   0.024   0.035   0.012   0.004   0.039   0.032   0.053   0.009   0.018   0.008   0.126   0.424   0.002   0.015   0.056
   0.018   0.010   0.014   0.014   0.000   0.014   0.016   0.008   0.005   0.015   0.031   0.018   0.011   0.037   0.000   0.019   0.011   0.688   0.049   0.022
   0.027   0.012   0.010   0.018   0.000   0.007   0.011   0.020   0.028   0.004   0.028   0.004   0.010   0.128   0.003   0.021   0.024   0.000   0.635   0.011
   0.056   0.004   0.015   0.011   0.007   0.006   0.017   0.007   0.005   0.146   0.112   0.018   0.017   0.022   0.015   0.023   0.048   0.003   0.007   0.463
//
H BLAJ010101
D Matrix built from structural superposition data for identifying potential
  remote homologues (Blake-Cohen, 2001)
R PMID:11254392
A Blake, J.D. and Cohen, F.E.
T Pairwise sequence alignment below the twilight zone
J J Mol Biol. 307, 721-735 (2001)
M rows = ARNDCQEGHILKMFPSTWYV, cols = ARNDCQEGHILKMFPSTWYV
       9
       0      14
       0       1      11
       0      -2       5      17
      -5     -16     -13     -13      39
       1       7       1       1     -14      13
       0       3       1       5     -20       5      12
       1      -2       1       2     -15      -3       0      16
      -2       2       5       1     -18       2       0      -2      23
       0      -7      -8      -9      -3      -7      -8      -3      -4      10
      -2      -4      -7     -10     -11     -10      -8      -6      -4       7      10
       0       7       2       0     -23       4       6       0       1      -7      -4       9
      -2      -8      -6      -7      -9      -8      -6      -7      -5      10      11      -4      13
      -1      -6      -3      -6     -12      -4     -10      -8      -1       3       3      -8       0      16
      -1      -3      -1       2     -18      -4      -1       0      -4      -3       1       1      -4      -4      19
       0       2       3       0     -18       0       0       0       0      -6      -4       1      -7      -4       1       9
      -3       0       2       0     -19       2       3      -4       0      -3      -5       1      -3      -2      -1       5       7
     -11      -6      -9      -7     -24     -12      -3     -10      -9      -6       2      -7      -4       9      -5      -7       0      32
      -3      -1       1      -6      -1      -5      -5     -10       1      -2      -4      -5      -3       8      -8      -1       3       0      19
       0      -4      -4     -10       0      -2      -6      -5      -6       8       6      -6       6       1      -4      -5      -1      -5      -1       9
//
H PRLA000101
D Structure derived matrix (SDM) for alignment of distantly related sequences
  (Prlic et al., 2000)
R PMID:10964983
A Prlic, A., Domingues, F.S. and Sippl, M.J.
T Structure-derived substitution matrices for alignment of distantly 
  related sequences
J Protein Eng. 13, 545-550 (2000)
M rows = ARNDCQEGHILKMFPSTWYV, cols = ARNDCQEGHILKMFPSTWYV
    2.09
   -0.50    2.87
   -0.57    0.60    3.60
   -0.73    0.13    1.78    4.02
    0.33   -1.30   -2.08   -2.51    6.99
   -0.75    0.13    0.33    0.34   -0.83    2.60
   -0.12    0.99   -0.16    1.20   -1.97    1.23    2.97
    0.27   -0.96    0.79   -1.20   -2.11   -0.12   -0.41    4.36
   -1.42    0.54    0.76   -0.01   -1.50   -0.46   -0.62   -0.40    5.89
   -0.97   -1.40   -2.43   -2.77    0.13   -1.47   -1.81   -2.93   -1.76    2.76
   -0.39   -1.19   -2.10   -2.65   -0.31   -1.49   -2.11   -1.98   -0.93    1.56    2.43
   -0.38    1.42    0.83    0.66   -2.19    0.92    1.11   -0.71    0.31   -1.81   -1.96    2.91
   -0.04   -0.63   -2.01   -2.58    1.04   -0.13   -1.86   -1.86   -1.04    0.99    1.61   -1.62    3.75
   -0.76   -1.40   -2.25   -2.19    1.13   -2.31   -1.61   -2.67   -0.22    0.76    1.23   -2.41    0.80    3.28
   -0.53    0.21   -1.10    0.72   -2.19    0.24   -0.26   -0.04   -1.44   -2.00   -1.56   -0.19   -1.09   -0.91    5.45
    0.34   -0.06    0.40    0.71    0.31    1.04    0.31    0.29   -0.74   -1.75   -2.30   -0.06   -1.34   -1.11   -0.29    2.36
    0.13   -0.15    0.30   -0.75   -0.59    0.60   -0.21   -0.81   -0.52   -0.96   -0.86   -0.10   -1.58   -0.69    0.93    1.20    2.04
   -0.66   -0.04   -2.89   -1.91   -0.76   -0.81   -2.70   -1.21   -1.48    0.25   -0.14   -1.94    0.87    2.29   -5.34   -1.18   -0.57    6.96
   -1.25   -0.75   -0.36   -1.21    0.13   -0.61   -1.64   -1.62   -0.12    0.08    0.70   -1.72   -0.41    1.96   -1.98   -1.56   -0.41    2.15    3.95
    0.02   -1.52   -2.17   -2.02    0.34   -1.38   -1.84   -1.96   -0.35    1.94    0.81   -1.27    0.61    0.51   -1.11   -1.11    0.05   -1.09    0.21    2.05
//
H PRLA000102
D Homologous structure dereived matrix (HSDM) for alignment of distantly
  related sequences (Prlic et al., 2000)
R PMID:10964983
A Prlic, A., Domingues, F.S. and Sippl, M.J.
T Structure-derived substitution matrices for alignment of distantly 
  related sequences
J Protein Eng. 13, 545-550 (2000)
M rows = ARNDCQEGHILKMFPSTWYV, cols = ARNDCQEGHILKMFPSTWYV
    5.50
   -2.24    8.59
   -1.77    0.24   10.00
   -2.38   -0.33    4.07   11.01
    0.45   -6.29   -6.53   -6.98   19.05
   -2.16   -0.74    1.42    1.10   -2.47    7.85
   -0.47    2.83   -0.39    2.41   -4.70    3.16    8.43
    0.63   -3.39    1.16   -3.91   -5.70   -0.24   -1.80   11.64
   -3.01    0.70    1.77    0.32   -5.95   -2.24   -1.29   -1.24   15.72
   -1.72   -3.93   -5.78   -6.18   -0.13   -3.26   -5.89   -8.58   -4.44    6.74
   -1.09   -2.83   -5.64   -7.41   -0.82   -4.56   -5.62   -6.55   -2.49    3.86    6.38
   -1.22    3.89    1.64    1.53   -6.65    3.24    3.08   -1.82   -0.17   -4.82   -5.91    8.23
    0.16   -1.43   -4.67   -7.88    3.50   -1.76   -3.94   -5.29   -3.66    2.94    4.32   -5.47   10.21
   -2.42   -4.36   -6.22   -5.06    1.72   -5.54   -4.44   -7.46    0.25    2.30    3.90   -6.19    2.66    9.14
   -1.11    1.31   -3.23    0.81   -6.70    1.30   -0.43   -1.79   -3.55   -4.04   -2.88   -1.21   -2.02   -2.96   13.32
    1.27   -0.50    1.54    2.34    1.08    2.59    0.42    0.63   -2.38   -4.67   -6.22   -0.27   -3.92   -5.03   -1.28    6.35
    0.60    0.34    1.14   -1.36   -1.89    1.08   -0.61   -2.24   -1.14   -3.03   -2.40   -0.37   -5.18   -4.00    2.44    3.09    6.33
   -2.61    1.02   -6.29   -5.63   -3.01   -4.30   -6.28   -4.77   -5.71   -0.26   -0.58   -5.45    4.28    6.49  -11.46   -4.44   -3.55   18.08
   -4.22   -1.01   -0.93   -3.85   -0.44   -1.73   -4.50   -4.34    1.17   -0.08    1.81   -4.03   -4.95    5.38   -7.41   -4.17   -2.92    6.79   10.92
    0.16   -3.80   -5.65   -6.10    1.32   -4.97   -4.23   -5.32   -1.63    5.23    2.28   -3.57    1.18    0.52   -2.31   -2.69   -0.23   -2.13    0.66    5.28
//
H DOSZ010101
D Amino acid similarity matrix based on the sausage force
  field (Dosztanyi-Torda, 2001)
R PMID:11524370
A Dosztanyi, Z. and Torda, A.E.
T Amino acid similarity matrices based on force fields
J Bioinformatics. 17, 686-699 (2001)
* #SM_SAUSAGE
* #Amino acid similarity matrix based on the sausage force field
* #Supplementary material
* #http://www.rsc.anu.edu.au/~zsuzsa/suppl/matrices/SM_SAUSAGE
* #Zsuzsanna Doszt?yi and Andrew E. Torda
* #Amino acid similarity matrices based on force fields
* #The amino acids are ordered according to the first principal component of the SM_SAUSAGE matrix.
* #The native cysteine residues were devided into two subsets depending on  their covalent state. 
* #Three rows correspond to cysteines: disulfide bonded (O), free cysteines (J) and all cysteines (C).
M rows = ARNDCQEGHILKMFPSTWYVJO, cols = ARNDCQEGHILKMFPSTWYV
    15.4    -4.9    -8.1   -10.7    38.6    -7.4   -10.7    -6.0     0.2    23.0    20.9   -10.9    17.8    18.9    -9.3    -1.6    -5.2    17.6    18.9    23.7
     6.4    -3.1    -5.3    -9.0    23.8    -6.5   -10.0    -8.3    -1.1    12.3    10.4    -7.9     9.6     9.8    -8.8    -2.1    -5.5     8.6    10.8    14.6
     4.0    -6.1    -3.4    -4.8    23.5    -7.2    -9.2    -7.6    -1.9     8.6     7.1   -10.1     6.2     7.8    -8.7    -1.3    -5.2     6.4     9.5    11.5
     4.1    -7.2    -2.7     0.2    22.2    -6.5    -6.0    -7.1    -2.7     5.3     4.8   -10.6     4.4     5.7    -8.2    -0.1    -4.9     4.6     8.0     8.1
    19.2    -6.6    -7.0    -7.4   111.4    -6.3   -12.2    -3.0    11.4    31.0    27.4   -12.3    26.1    35.3     0.2     2.6     1.5    25.9    30.3    31.5
     6.3    -4.8    -5.3    -6.8    24.0    -6.0    -8.3    -8.4    -1.4    11.2    10.0    -8.9     8.9     9.2    -9.0    -2.8    -6.1     8.3    10.4    13.1
     5.3    -5.3    -4.5    -3.7    21.3    -5.8    -6.0    -7.7    -1.8     8.7     7.4    -9.1     6.7     7.4    -7.9    -2.3    -5.8     6.8     8.7    10.8
     7.3    -8.2    -6.9    -8.4    30.7    -9.0   -10.8     1.2    -2.9     7.8     6.0   -11.6     7.1     8.8    -7.1    -1.5    -7.3     8.4     9.8    11.1
     6.8    -6.0    -6.1    -8.0    30.5    -7.8   -10.7    -7.5    -0.7    14.1    11.8   -10.5    10.5    12.3    -8.2    -2.4    -5.7     9.8    13.2    16.1
    12.7    -5.6   -11.3   -15.0    39.5    -9.0   -13.5   -12.7     0.6    35.7    29.5   -12.6    22.8    25.3    -8.9    -6.2    -4.7    21.3    24.1    35.5
    13.0    -5.7   -10.1   -13.3    39.5    -8.2   -12.4   -11.5     0.9    31.9    27.8   -12.3    21.8    23.6    -9.2    -5.1    -5.3    20.1    22.3    31.1
     5.3    -3.0    -4.4    -7.3    20.3    -5.7    -8.7    -7.3    -1.5     8.5     7.0    -6.7     7.2     7.0    -8.2    -1.7    -5.6     5.8     8.1    10.9
    11.2    -5.6    -8.8   -11.6    36.3    -7.7   -11.4   -10.3     0.5    25.5    22.4   -11.2    18.8    19.4    -8.7    -4.2    -5.7    17.3    19.0    25.7
    11.4    -6.5    -9.3   -11.9    39.2    -8.7   -12.5    -9.4     0.4    27.2    23.2   -12.2    18.9    21.5    -8.0    -4.1    -5.3    18.4    21.0    27.5
     4.9    -7.8    -7.3    -7.5    26.7    -8.5   -10.0    -6.2    -1.2    12.5     9.1   -10.4     8.2    10.1     2.0    -2.1    -5.3     8.9    10.0    14.3
     7.3    -5.9    -4.3    -4.9    28.2    -7.1    -9.3    -5.3    -1.6     8.8     7.9   -10.0     7.8     8.9    -7.1     3.0    -3.0     7.6    10.5    11.7
     6.7    -5.4    -5.2    -7.0    27.1    -7.3   -10.1    -8.0    -1.5    13.6    10.9   -10.1     9.3    11.0    -7.3     0.8    -2.6     9.0    12.3    16.2
     9.9    -6.9    -8.8   -10.7    37.4    -8.6   -11.7    -9.0    -0.3    23.2    19.7   -12.1    16.2    18.4    -7.4    -3.8    -5.5    17.0    19.1    23.8
    10.2    -6.5    -8.6   -10.7    37.4    -8.4   -11.6    -8.8    -0.0    23.7    19.9   -11.7    16.6    19.1    -7.7    -3.9    -5.3    16.9    19.8    24.6
    13.4    -5.4   -10.7   -14.8    41.3    -8.6   -13.4   -11.4     1.0    35.9    29.2   -12.6    23.0    26.0    -8.4    -5.5    -3.9    22.1    25.1    36.7
    14.8    -7.1   -10.4   -13.9    48.4    -9.3   -13.4    -8.9     1.0    30.8    27.0   -13.5    23.1    25.1   -10.1    -3.1    -4.6    21.6    24.9    31.8
    24.8    -4.6    -3.2    -1.4   166.7    -1.7   -10.1     4.6    20.6    31.6    28.3    -9.3    29.4    44.3    10.4     8.8     7.5    30.9    36.2    32.3
//
H DOSZ010102
D Normalised version of SM_SAUSAGE (Dosztanyi-Torda, 2001)
R PMID:11524370
A Dosztanyi, Z. and Torda, A.E.
T Amino acid similarity matrices based on force fields
J Bioinformatics. 17, 686-699 (2001)
* #SM_SAUS_NORM
* #Normalised version of SM_SAUSAGE
* #For each matrix element of SM_SAUSAGE, the average over its column and row were subtracted.
* #Supplementary material
* #http://www.rsc.anu.edu.au/~zsuzsa/suppl/matrices/SM_SAUS_NORM
* #Zsuzsanna Doszt?yi and Andrew E. Torda
* #Amino acid similarity matrices based on force fields
* #The amino acids are ordered according to the first principal component of the SM_SAUSAGE matrix.
M rows = ARNDCQEGHILKMFPSTWYV, cols = ARNDCQEGHILKMFPSTWYV
    0.56   -5.10   -7.00   -7.73    0.83   -5.75   -6.26   -4.00   -5.12   -1.42   -0.71   -6.17   -1.44   -1.90   -7.45   -5.11   -6.13   -1.22   -2.38   -2.26
   -4.35    0.78   -0.16   -1.92   -9.95   -0.76   -1.47   -2.26   -2.33   -8.02   -7.13    0.93   -5.59   -6.89   -2.89   -1.52   -2.29   -6.20   -6.44   -7.30
   -5.77   -1.19    2.69    3.20   -9.21   -0.47    0.31   -0.51   -2.20  -10.75   -9.48   -0.26   -8.00   -7.97   -1.81    0.24   -1.08   -7.43   -6.70   -9.36
   -5.30   -1.93    3.82    8.58  -10.18    0.63    3.96    0.39   -2.59  -13.72  -11.35   -0.39   -9.45   -9.67   -0.94    1.79   -0.32   -8.82   -7.82  -12.42
   -1.72   -8.93  -11.04  -12.59    8.91   -9.31  -10.67   -8.60   -5.98    4.64    3.68  -10.42    2.17    2.61  -10.05   -8.27   -7.21    1.05    1.86    4.11
   -4.22   -0.66    0.14    0.51   -9.50   -0.05    0.50   -2.03   -2.34   -8.94   -7.32    0.13   -6.00   -7.28   -2.89   -1.96   -2.68   -6.16   -6.52   -8.49
   -4.66   -0.60    1.40    4.09  -11.62    0.74    3.35   -0.89   -2.27  -10.89   -9.31    0.49   -7.69   -8.51   -1.29   -1.00   -1.81   -7.23   -7.74  -10.31
   -2.72   -3.58   -1.07   -0.67   -2.34   -2.60   -1.59    7.98   -3.42  -11.80  -10.82   -2.10   -7.33   -7.17   -0.52   -0.24   -3.37   -5.61   -6.74  -10.01
   -4.62   -2.70   -1.65   -1.56   -3.85   -2.73   -2.77   -2.09   -2.55   -6.88   -6.34   -2.36   -5.32   -5.02   -2.94   -2.48   -3.13   -5.59   -4.71   -6.44
   -3.54   -7.10  -11.57  -13.36    0.31   -8.69  -10.38  -12.05   -6.06    9.92    6.53   -9.26    2.19    3.12   -8.48  -11.11   -6.99    1.12    1.50    8.16
   -2.74   -6.81   -9.98  -11.26    0.73   -7.44   -8.85  -10.47   -5.34    6.58    5.26   -8.48    1.62    1.91   -8.38   -9.58   -7.08    0.30    0.07    4.19
   -4.52    1.87    1.66    0.73  -12.46    0.93    0.77   -0.31   -1.81  -10.93   -9.60    3.01   -7.07   -8.79   -1.43   -0.17   -1.43   -8.02   -8.13  -10.05
   -3.19   -5.33   -7.25   -8.13   -1.06   -5.56   -6.49   -7.84   -4.34    1.59    1.24   -5.99   -0.02   -0.91   -6.45   -7.27   -6.08   -1.10   -1.77    0.20
   -3.42   -6.69   -8.26   -8.93    1.34   -7.06   -8.01   -7.42   -4.96    2.74    1.57   -7.53   -0.35    0.74   -6.23   -7.68   -6.23   -0.50   -0.36    1.52
   -5.95   -3.94   -2.26   -0.52   -7.12   -2.87   -1.51   -0.20   -2.55   -7.90   -8.52   -1.66   -7.10   -6.65    7.75   -1.58   -2.20   -5.96   -7.30   -7.69
   -3.67   -2.18    0.63    1.90   -5.80   -1.63   -0.97    0.58   -3.10  -11.75   -9.84   -1.38   -7.62   -8.02   -1.44    3.35   -0.07   -7.36   -6.95  -10.43
   -4.77   -2.16   -0.75   -0.62   -7.27   -2.26   -2.25   -2.58   -3.43   -7.48   -7.34   -1.98   -6.61   -6.42   -2.08    0.71   -0.11   -6.41   -5.58   -6.35
   -3.91   -6.07   -6.74   -6.70    0.60   -5.95   -6.26   -5.99   -4.57   -0.27   -0.92   -6.32   -2.01   -1.37   -4.55   -6.28   -5.42   -0.78   -1.14   -1.09
   -3.88   -5.94   -6.73   -6.96    0.33   -5.99   -6.32   -6.07   -4.56    0.05   -0.99   -6.20   -1.90   -0.88   -5.16   -6.67   -5.43   -1.14   -0.77   -0.54
   -3.35   -7.47  -11.62  -13.79    1.58   -8.92  -10.84  -11.38   -6.24    9.49    5.63   -9.80    1.76    3.32   -8.51  -10.91   -6.70    1.31    1.87    8.82
//
H DOSZ010103
D An amino acid similarity matrix based on the THREADER force field
  (Dosztanyi-Torda, 2001)
R PMID:11524370
A Dosztanyi, Z. and Torda, A.E.
T Amino acid similarity matrices based on force fields
J Bioinformatics. 17, 686-699 (2001)
* #SM_THREADER
* #An amino acid similarity matrix based on the THREADER force field (Jones, DT et al.Nature, 358,86-89).
* #Supplementary material
* #http://www.rsc.anu.edu.au/~zsuzsa/suppl/matrices/SM_THREADER
* #Zsuzsanna Doszt?yi and Andrew E. Torda
* #Amino acid similarity matrices based on force fields
* #The amino acids are ordered according to the first principal component of the SM_SAUSAGE matrix.
M rows = ARNDCQEGHILKMFPSTWYV, cols = ARNDCQEGHILKMFPSTWYV
    10.0    -0.2    -1.2    -2.8     3.8     0.6    -1.0     0.9     0.2     5.1     4.5    -1.4     3.9     1.9    -0.9     1.8     1.6     0.5     1.8     5.5
     2.3     8.1    -0.4    -1.6    -0.6     2.9     1.0    -1.9     1.8     0.5     1.8     3.6     1.7     0.4    -2.1     0.2     0.7    -0.5     1.7     1.0
     1.5     0.3     6.4     1.9    -0.3     1.2     0.6     0.5     2.0    -0.4    -1.1     0.5     0.2    -1.9    -1.3     1.6     1.0    -2.4    -0.4    -0.6
     0.7    -0.4     2.2     7.3    -2.3     1.5     2.7    -0.4     0.2    -1.6    -1.3    -0.1    -1.7    -3.0    -0.4     0.9     0.2    -3.4    -1.4    -1.8
     2.7    -3.0    -2.4    -4.9    16.3    -2.4    -4.1    -1.6    -0.9     4.0     3.7    -4.2     2.2     2.7    -3.6    -0.4     0.5    -1.2     1.0     4.6
     3.5     3.2     0.8     0.6     0.0     8.4     3.3    -1.0     2.7     1.2     2.6     3.1     3.4    -0.6    -0.2     1.3     0.8     1.2     1.6     0.7
     3.0     2.2     0.8     2.4    -0.6     4.1     7.0    -1.9     1.6    -0.3     1.0     2.3     1.1    -0.4    -0.2     0.4     0.7    -1.0     0.2     0.2
     2.0    -2.2    -0.1    -1.3    -1.0    -1.3    -3.0     7.8    -0.9    -1.2    -1.4    -2.2    -0.9    -1.9    -1.5     0.6    -0.9    -1.7    -1.3    -1.3
     1.4     1.1     0.8    -1.4     0.4     1.8    -0.2    -1.0     9.9     0.5     1.4    -0.2     2.1     2.0    -1.6    -0.2    -0.4    -0.6     4.1     0.3
     4.1    -2.9    -3.8    -5.9     4.8    -2.4    -5.7    -2.5    -1.2    13.2     9.8    -4.7     7.4     6.3    -3.1    -2.2     1.1     1.6     4.0    11.8
     3.6    -1.4    -4.3    -5.4     4.2    -0.8    -3.9    -2.7    -0.4     9.7    12.5    -3.9     8.3     6.8    -3.8    -2.1     0.9     2.3     3.8     8.2
     2.7     4.6     0.8    -0.3    -0.7     3.9     2.4    -1.0     1.6     0.4     0.8     6.5     1.0    -1.3    -0.2     1.2     0.6    -1.1     0.2     0.0
     4.3    -0.4    -2.2    -4.9     3.6     1.2    -2.5    -1.7     1.3     8.7     9.7    -2.5    11.4     5.2    -2.8    -1.0     0.9     2.7     4.1     7.2
     1.8    -2.0    -4.4    -6.3     3.8    -3.1    -4.3    -2.6     1.1     7.0     7.6    -5.1     4.8    12.4    -3.8    -2.2    -0.1     4.4     7.6     5.8
     0.3    -2.1    -1.5    -0.8    -2.9    -0.4    -0.7    -1.2    -1.1    -1.5    -2.4    -0.9    -1.7    -2.7     8.7    -0.4    -0.2    -3.1    -1.9    -1.5
     3.5     0.0     0.9    -0.3     1.3     0.9    -0.8     0.6     0.3     0.4     0.4    -0.1     0.6    -0.4    -0.6     4.9     2.8    -2.0     0.1     1.1
     2.9     0.1    -0.1    -1.4     2.1    -0.0    -1.1    -1.0    -0.3     3.2     2.9    -1.1     2.0     1.1    -0.6     2.4     5.8    -0.7     0.7     3.9
     1.5    -1.8    -4.2    -5.9     0.6    -0.3    -3.8    -2.0    -0.7     3.5     4.3    -3.9     3.5     5.5    -3.7    -3.0    -1.2    16.0     5.4     3.1
     2.2    -0.1    -2.5    -4.2     2.4    -0.4    -3.1    -1.9     3.6     5.4     5.1    -3.0     4.3     8.2    -2.9    -1.3    -0.2     4.9    10.8     5.1
     4.6    -2.2    -3.8    -5.9     5.4    -2.6    -4.9    -2.5    -1.4    11.9     8.4    -4.8     6.1     5.1    -3.0    -1.4     2.0     1.3     3.8    12.7
//
H DOSZ010104
D Normalised version of SM_THREADER (Dosztanyi-Torda, 2001)
R PMID:11524370
A Dosztanyi, Z. and Torda, A.E.
T Amino acid similarity matrices based on force fields
J Bioinformatics. 17, 686-699 (2001)
* #SM_THREAD_NORM
* #Normalised version of SM_THREADER 
* #based on the THREADER force field (Jones, DT et al.Nature, 358,86-89)
* #For each matrix element of SM_THREADER, the average over its column and row were subtracted.
* #Supplementary material
* #http://www.rsc.anu.edu.au/~zsuzsa/suppl/matrices/SM_THREAD_NORM
* #Zsuzsanna Doszt?yi and Andrew E. Torda
* #Amino acid similarity matrices based on force fields
* #The amino acids are ordered according to the first principal component of the SM_SAUSAGE matrix.
M rows = ARNDCQEGHILKMFPSTWYV, cols = ARNDCQEGHILKMFPSTWYV
    5.34   -2.01   -2.01   -2.43    0.01   -1.75   -1.66   -0.02   -2.48   -0.08   -0.70   -1.99   -0.84   -2.14   -1.29    0.01   -0.96   -2.08   -2.19    0.48
   -1.67    7.03   -0.49   -0.60   -3.62    1.22    1.10   -2.07   -0.20   -3.98   -2.76    3.65   -2.34   -2.93   -1.78   -0.86   -1.15   -2.34   -1.64   -3.36
   -1.90   -0.19    6.86    3.48   -2.83    0.13    1.27    0.93    0.53   -4.39   -5.08    1.17   -3.28   -4.64   -0.37    1.09   -0.27   -3.75   -3.14   -4.39
   -2.11   -0.33    3.25    9.44   -4.24    0.92    3.93    0.59   -0.65   -4.98   -4.75    1.13   -4.55   -5.14    1.12    0.90   -0.56   -4.19   -3.58   -4.97
   -0.65   -3.48   -1.98   -3.34   13.84   -3.45   -3.46   -1.20   -2.28    0.06   -0.27   -3.54   -1.22   -0.03   -2.65   -0.95   -0.79   -2.50   -1.78    0.87
   -1.30    1.31   -0.14    0.78   -3.78    5.96    2.62   -1.93   -0.10   -4.13   -2.74    2.36   -1.42   -4.69   -0.67   -0.59   -1.87   -1.51   -2.55   -4.38
   -1.02    0.98    0.60    3.37   -3.78    2.32    6.97   -2.17   -0.47   -4.95   -3.65    2.26   -2.97   -3.79    0.06   -0.76   -1.28   -3.04   -3.19   -4.26
   -0.26   -1.56    1.55    1.48   -2.34   -1.25   -1.17    9.29   -1.15   -4.03   -4.21   -0.44   -3.19   -3.47    0.51    1.17   -1.03   -1.86   -2.90   -3.91
   -2.56    0.01    0.68   -0.35   -2.57    0.11   -0.10   -1.19    7.89   -3.96   -3.16   -0.08   -1.90   -1.24   -1.20   -1.23   -2.21   -2.46    0.77   -4.03
   -0.31   -4.43   -4.41   -5.36    1.30   -4.51   -6.08   -3.12   -3.69    8.26    4.84   -5.08    2.88    2.56   -3.16   -3.78   -1.20   -0.79    0.26    7.02
   -0.88   -3.07   -4.99   -4.92    0.62   -3.02   -4.35   -3.46   -2.92    4.66    7.42   -4.37    3.75    2.96   -4.05   -3.72   -1.49   -0.14   -0.11    3.28
   -1.38    3.49    0.60    0.70   -3.80    2.13    2.39   -1.25   -0.51   -4.23   -3.83    6.56   -3.10   -4.67    0.10   -0.01   -1.31   -3.05   -3.23   -4.37
   -0.78   -2.55   -3.44   -4.93   -0.53   -1.56   -3.50   -2.97   -1.76    3.06    4.06   -3.56    6.28    0.83   -3.50   -3.15   -2.07   -0.25   -0.27    1.80
   -2.29   -3.14   -4.59   -5.31    0.64   -4.86   -4.31   -2.90   -0.99    2.42    2.96   -5.13    0.69    8.98   -3.57   -3.35   -2.07    2.45    4.24    1.36
   -1.73   -1.24    0.29    2.15   -3.99   -0.11    1.26    0.50   -1.21   -4.07   -4.99    1.11   -3.74   -4.08   11.00    0.46   -0.15   -3.03   -3.33   -3.88
   -0.12   -0.69    1.10    1.03   -1.37   -0.44   -0.42    0.78   -1.31   -3.73   -3.79    0.30   -3.04   -3.34    0.06    4.20    1.29   -3.55   -2.88   -2.85
   -1.04   -0.99   -0.21   -0.43   -0.96   -1.67   -1.06   -1.15   -2.26   -1.36   -1.66   -1.06   -2.03   -2.16   -0.27    1.33    3.91   -2.63   -2.66   -0.44
   -2.06   -2.46   -3.91   -4.46   -2.06   -1.62   -3.37   -1.76   -2.37   -0.62    0.12   -3.41   -0.13    2.53   -2.97   -3.71   -2.67   14.53    2.44   -0.84
   -2.32   -1.76   -3.17   -3.78   -1.25   -2.67   -3.59   -2.64    0.97    0.27   -0.02   -3.54   -0.32    4.28   -3.11   -2.98   -2.64    2.44    6.90    0.15
    0.27   -3.71   -4.37   -5.30    1.94   -4.67   -5.26   -3.06   -3.82    7.00    3.43   -5.11    1.69    1.39   -3.05   -2.86   -0.24   -1.03    0.05    7.93
//
H GIAG010101
D Residue substitutions matrix from thermo/mesophilic to psychrophilic
  enzymes (Gianese et al., 2001)
R PMID:11342709
A Gianese, G., Argos, P. and Pascarella, S.
T Structural adaptation of enzymes to low temperatures
J Protein Eng. 14, 141-148 (2001)
* (rows = WARM, cols = COLD)
M rows = ARNDCQEGHILKMFPSTWYV, cols = ARNDCQEGHILKMFPSTWYV
     0.0    -2.4     0.5    -1.0    -0.4    -0.1    -5.7     1.8    -0.2    -0.8     0.5    -1.8     0.2    -0.2    -2.0    -0.4     0.9    -0.4    -0.4    -3.9
     2.4     0.0     2.1     0.9     0.2     2.0     0.9     0.8     0.1     0.2     0.5     3.4     0.1    -0.5     0.5     2.2     1.3     0.2     0.2     0.7
    -0.5    -2.1     0.0    -1.3     0.2    -0.8    -1.9    -0.4    -0.3    -0.2    -0.5    -2.4    -0.2    -0.4    -0.8    -1.3    -1.5     0.0     0.4    -0.9
     1.0    -0.9     1.3     0.0    -0.2    -1.2    -2.7    -1.0    -0.2     0.0    -0.8    -0.7     0.1    -0.1    -0.6    -0.3     1.2    -0.2    -0.1     0.1
     0.4    -0.2    -0.2     0.2     0.0     0.1    -0.3    -0.3     0.1    -0.1     0.2     0.0     0.0     0.0     0.0     0.0    -0.9    -0.1     0.1    -0.6
     0.1    -2.0     0.8     1.2    -0.1     0.0    -1.5    -0.5     0.4    -0.5    -1.4    -1.9     0.5    -0.3    -0.3     0.1     0.7    -0.2     0.0    -0.8
     5.7    -0.9     1.9     2.7     0.3     1.5     0.0     0.0    -0.4     0.5    -0.4    -1.7     0.4    -0.1    -0.7     2.7     2.2    -0.2    -0.1    -0.1
    -1.8    -0.8     0.4     1.0     0.3     0.5     0.0     0.0     0.2     0.0    -0.1    -0.5     0.4    -0.5    -0.2     0.1    -0.1    -0.1     0.3     0.4
     0.2    -0.1     0.3     0.2    -0.1    -0.4     0.4    -0.2     0.0     0.1     0.3    -0.4     0.0    -0.5     0.2     0.3     0.0    -0.3    -0.3     0.1
     0.8    -0.2     0.2     0.0     0.1     0.5    -0.5     0.0    -0.1     0.0    -0.3    -0.6     1.3    -0.2     0.2     0.3     0.8    -0.5     0.0    -2.1
    -0.5    -0.5     0.5     0.8    -0.2     1.4     0.4     0.1    -0.3     0.3     0.0    -0.7     0.2    -1.0     0.6    -0.1    -0.1     0.1    -0.7     0.1
     1.8    -3.4     2.4     0.7     0.0     1.9     1.7     0.5     0.4     0.6     0.7     0.0     0.8    -0.7     0.1     2.6     1.4     0.0     0.1     1.1
    -0.2    -0.1     0.2    -0.1     0.0    -0.5    -0.4    -0.4     0.0    -1.3    -0.2    -0.8     0.0     0.3    -0.2    -0.2     0.1     0.2    -0.1    -1.0
     0.2     0.5     0.4     0.1     0.0     0.3     0.1     0.5     0.5     0.2     1.0     0.7    -0.3     0.0     0.0     0.5    -0.8    -0.7     0.5     0.3
     2.0    -0.5     0.8     0.6     0.0     0.3     0.7     0.2    -0.2    -0.2    -0.6    -0.1     0.2     0.0     0.0     1.8     0.5    -0.1     0.1     0.2
     0.4    -2.2     1.3     0.3     0.0    -0.1    -2.7    -0.1    -0.3    -0.3     0.1    -2.6     0.2    -0.5    -1.8     0.0    -1.6    -0.1    -0.1     0.0
    -0.9    -1.3     1.5    -1.2     0.9    -0.7    -2.2     0.1     0.0    -0.8     0.1    -1.4    -0.1     0.8    -0.5     1.6     0.0    -0.4     0.4    -1.5
     0.4    -0.2     0.0     0.2     0.1     0.2     0.2     0.1     0.3     0.5    -0.1     0.0    -0.2     0.7     0.1     0.1     0.4     0.0    -0.2     0.1
     0.4    -0.2    -0.4     0.1    -0.1     0.0     0.1    -0.3     0.3     0.0     0.7    -0.1     0.1    -0.5    -0.1     0.1    -0.4     0.2     0.0    -0.1
     3.9    -0.7     0.9    -0.1     0.6     0.8     0.1    -0.4    -0.1     2.1    -0.1    -1.1     1.0    -0.3    -0.2     0.0     1.5    -0.1     0.1     0.0
//
H DAYM780302
D Log odds matrix for 40 PAMs (Dayhoff et al., 1978)
R
A Dayhoff, M.O., Schwartz, R.M. and Orcutt, B.C.
T A model of evolutionary change in proteins
J 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)
* #
* # This matrix was produced by "pam" Version 1.0.6 [28-Jul-93]
* #
* # PAM 40 substitution matrix, scale = ln(2)/2 = 0.346574
* #
* # Expected score = -4.27, Entropy = 2.26 bits
* #
* # Lowest score = -15, Highest score = 13
* #
M rows = ARNDCQEGHILKMFPSTWYV-, cols = ARNDCQEGHILKMFPSTWYV
       6      -6      -3      -3      -6      -3      -2      -1      -6      -4      -5      -6      -4      -7      -1       0       0     -12      -7      -2
      -6       8      -5      -9      -7      -1      -8      -8      -1      -5      -8       1      -3      -8      -3      -2      -5      -1      -9      -7
      -3      -5       7       2      -9      -3      -1      -2       1      -4      -6       0      -7      -8      -5       0      -1      -7      -4      -7
      -3      -9       2       7     -12      -2       3      -3      -3      -6     -11      -4      -9     -13      -7      -3      -4     -13     -10      -7
      -6      -7      -9     -12       9     -12     -12      -8      -7      -5     -13     -12     -12     -11      -7      -2      -7     -14      -3      -5
      -3      -1      -3      -2     -12       8       2      -6       1      -7      -4      -2      -3     -11      -2      -4      -5     -11     -10      -6
      -2      -8      -1       3     -12       2       7      -3      -4      -5      -8      -4      -6     -12      -5      -4      -5     -15      -8      -6
      -1      -8      -2      -3      -8      -6      -3       6      -8      -9      -9      -6      -7      -8      -5      -1      -5     -13     -12      -5
      -6      -1       1      -3      -7       1      -4      -8       9      -8      -5      -5      -9      -5      -3      -5      -6      -6      -3      -6
      -4      -5      -4      -6      -5      -7      -5      -9      -8       8      -1      -5       0      -2      -7      -6      -2     -12      -5       2
      -5      -8      -6     -11     -13      -4      -8      -9      -5      -1       7      -7       1      -2      -6      -7      -6      -5      -6      -2
      -6       1       0      -4     -12      -2      -4      -6      -5      -5      -7       6      -1     -12      -6      -3      -2     -10      -8      -8
      -4      -3      -7      -9     -12      -3      -6      -7      -9       0       1      -1      11      -3      -7      -5      -3     -11     -10      -1
      -7      -8      -8     -13     -11     -11     -12      -8      -5      -2      -2     -12      -3       9      -9      -6      -8      -4       2      -7
      -1      -3      -5      -7      -7      -2      -5      -5      -3      -7      -6      -6      -7      -9       8      -1      -3     -12     -12      -5
       0      -2       0      -3      -2      -4      -4      -1      -5      -6      -7      -3      -5      -6      -1       6       1      -4      -6      -5
       0      -5      -1      -4      -7      -5      -5      -5      -6      -2      -6      -2      -3      -8      -3       1       7     -11      -6      -2
     -12      -1      -7     -13     -14     -11     -15     -13      -6     -12      -5     -10     -11      -4     -12      -4     -11      13      -4     -14
      -7      -9      -4     -10      -3     -10      -8     -12      -3      -5      -6      -8     -10       2     -12      -6      -6      -4      10      -6
      -2      -7      -7      -7      -5      -6      -6      -5      -6       2      -2      -8      -1      -7      -5      -5      -2     -14      -6       7
     -15     -15     -15     -15     -15     -15     -15     -15     -15     -15     -15     -15     -15     -15     -15     -15     -15     -15     -15     -15
//
H HENS920104
D BLOSUM50 substitution matrix (Henikoff-Henikoff, 1992)
R PMID:1438297
A Henikoff, S. and Henikoff, J.G.
T Amino acid substitution matrices from protein blocks
J Proc. Natl. Acad. Sci. USA 89, 10915-10919 (1992)
* #  Matrix made by matblas from blosum50.iij
* #  BLOSUM Clustered Scoring Matrix in 1/3 Bit Units
* #  Blocks Database = /data/blocks_5.0/blocks.dat
* #  Cluster Percentage: >= 50
* #  Entropy =   0.4808, Expected =  -0.3573
M rows = ARNDCQEGHILKMFPSTWYV, cols = ARNDCQEGHILKMFPSTWYV
       5      -2      -1      -2      -1      -1      -1       0      -2      -1      -2      -1      -1      -3      -1       1       0      -3      -2       0
      -2       7      -1      -2      -4       1       0      -3       0      -4      -3       3      -2      -3      -3      -1      -1      -3      -1      -3
      -1      -1       7       2      -2       0       0       0       1      -3      -4       0      -2      -4      -2       1       0      -4      -2      -3
      -2      -2       2       8      -4       0       2      -1      -1      -4      -4      -1      -4      -5      -1       0      -1      -5      -3      -4
      -1      -4      -2      -4      13      -3      -3      -3      -3      -2      -2      -3      -2      -2      -4      -1      -1      -5      -3      -1
      -1       1       0       0      -3       7       2      -2       1      -3      -2       2       0      -4      -1       0      -1      -1      -1      -3
      -1       0       0       2      -3       2       6      -3       0      -4      -3       1      -2      -3      -1      -1      -1      -3      -2      -3
       0      -3       0      -1      -3      -2      -3       8      -2      -4      -4      -2      -3      -4      -2       0      -2      -3      -3      -4
      -2       0       1      -1      -3       1       0      -2      10      -4      -3       0      -1      -1      -2      -1      -2      -3       2      -4
      -1      -4      -3      -4      -2      -3      -4      -4      -4       5       2      -3       2       0      -3      -3      -1      -3      -1       4
      -2      -3      -4      -4      -2      -2      -3      -4      -3       2       5      -3       3       1      -4      -3      -1      -2      -1       1
      -1       3       0      -1      -3       2       1      -2       0      -3      -3       6      -2      -4      -1       0      -1      -3      -2      -3
      -1      -2      -2      -4      -2       0      -2      -3      -1       2       3      -2       7       0      -3      -2      -1      -1       0       1
      -3      -3      -4      -5      -2      -4      -3      -4      -1       0       1      -4       0       8      -4      -3      -2       1       4      -1
      -1      -3      -2      -1      -4      -1      -1      -2      -2      -3      -4      -1      -3      -4      10      -1      -1      -4      -3      -3
       1      -1       1       0      -1       0      -1       0      -1      -3      -3       0      -2      -3      -1       5       2      -4      -2      -2
       0      -1       0      -1      -1      -1      -1      -2      -2      -1      -1      -1      -1      -2      -1       2       5      -3      -2       0
      -3      -3      -4      -5      -5      -1      -3      -3      -3      -3      -2      -3      -1       1      -4      -4      -3      15       2      -3
      -2      -1      -2      -3      -3      -1      -2      -3       2      -1      -1      -2       0       4      -3      -2      -2       2       8      -1
       0      -3      -3      -4      -1      -3      -3      -4      -4       4       1      -3       1      -1      -3      -2       0      -3      -1       5
//
H QUIB020101
D STROMA score matrix for the alignment of known distant homologs
  (Qian-Goldstein, 2002)
R PMID:12211027
A Qian, B. and Goldstein, R.A.
T Optimization of a new score function for the generation of accurate 
  alignments
J Proteins. 48, 605-610 (2002)
M rows = ARNDCQEGHILKMFPSTWYV, cols = ARNDCQEGHILKMFPSTWYV
     2.5
     0.2     5.2
     1.1     0.7     2.5
       1     0.1     3.3     5.3
     1.2    -1.3    -1.9    -3.1    11.5
    -0.1       2     1.9     1.1    -2.5     3.6
     1.2     1.9     2.3     3.2    -2.4     1.7     3.7
     1.4    -0.2     0.7     0.9    -1.3    -0.3     0.5     7.5
    -1.4     1.5     1.4     0.5    -1.7     1.4     0.3    -1.7     6.8
     0.3    -1.9    -2.4    -2.9    -3.2    -0.9    -3.1    -3.7    -1.8     4.5
    -0.2    -1.5    -2.4    -3.4    -1.6    -1.2    -1.5    -3.8    -2.4     3.4     5.2
    -0.2     3.4     1.6     1.4      -3     2.2     1.2     0.4     1.1    -1.5      -2     3.9
    -0.2    -1.4    -2.1    -2.8    -1.3    -0.6      -2    -3.8    -0.8     2.2     3.1    -0.5     5.4
    -1.6    -3.2    -2.5    -3.7    -0.8    -1.7   -13.7    -4.7    -0.9     2.2     3.7    -2.8     1.7       7
     0.7    -0.6    -0.1    -0.2    -3.6       1       0    -0.8    -2.1    -2.4    -1.4     0.2    -1.9    -4.1     8.1
     1.7     0.2     1.4     1.7     0.7     0.9     1.1     1.6    -0.1    -1.1    -0.8     1.4    -1.1    -2.5       2     2.8
     1.7     0.2     1.4     0.1     0.3    -0.1     1.6    -0.6    -0.2       0     0.3       1    -0.3    -0.8     1.1     2.6     0.4
    -3.3    -1.5      -4    -5.7    -0.5    -2.9    -4.7    -4.2    -1.2    -1.8    -1.2      -3    -0.6     3.7      -5    -2.8    -2.9    14.9
    -1.8    -0.9    -0.8    -2.9    -0.3    -1.5    -2.2    -4.8     2.9     0.2     0.8    -1.5     0.5     5.2    -3.3    -0.9    -0.8     4.9     8.1
     1.9    -2.8    -0.9    -2.5     0.7    -1.5    -1.3    -1.4    -2.5     4.5     3.4      -1     1.7     0.9    -1.1      -3     1.5    -2.5     0.3     4.2
//
H NAOD960101
D Substitution matrix derived from the single residue interchanges at spatially
  conserved regions of proteins (Naor et al., 1996)
R PMID:8601843
A Naor, D., Fischer, D., Jernigan, R.L., Wolfson, H.J. and Nussinov, R.
T Amino Acid Pair Interchanges at Spatially Conserved Locations (Naor et al)
J Journal of Molecular Biology 256, 924-938 (1996)
M rows = ARNDCQEGHILKMFPSTWYV, cols = ARNDCQEGHILKMFPSTWYV
       4
       0       7
       0       4       8
       0       4       8      11
       2      -5      -5      -4      14
       0       5       5       6      -4       7
       0       8       6       7      -6       8      11
       0       0       5       4       0       0       0      12
      -1       3       2       3      -2       1       2       3       5
      -2      -7      -9      -9       4      -7      -9      -7      -3      10
       0      -5      -7      -8       2      -5      -6      -6      -3       7       9
       0       9       6       7      -7       7       9       0       1      -9      -7      13
       0      -2      -3      -4       2      -2      -2      -3      -1       3       5      -4       4
      -1      -5      -6      -6       3      -5      -6      -3      -2       6       6      -7       3       6
       0       1       6       6      -1       1       0       6       2      -8      -8       3      -6      -4      19
       0       2       4       4      -3       2       3       4       2      -5      -5       3      -3      -4       3       5
       0       1       2       2      -2       1       3       0       0      -3      -3       2      -2      -2       1       2       3
       0      -3      -4      -4       0      -2      -3      -1      -1       4       2      -5       1       3      -5      -2       0       9
       0      -2      -2      -3       0      -1      -2      -1       0       2       1      -3       1       2      -3      -1       0       2       3
      -2      -6      -8      -9       4      -8      -9      -5      -2       9       5      -8       2       5      -5      -4      -1       4       2       9
//
H RUSR970101
D Substitution matrix based on structural alignments of analogous proteins
  (Russell et al., 1997)
R PMID:9199410
A Russell, R.B., Saqi, M.A.S., Sayle, R.A., Bates, P.A. and Sternberg, M.J.E.
T Recognition of analogous and homologous protein folds: Analysis of sequence
  and structure conservation
J Journal of Molecular Biology 269, 423-439 (1997)
M rows = ARNDCQEGHILKMFPSTWYV, cols = ARNDCQEGHILKMFPSTWYV
      -2
       1       0
       0       2       0
       0       3       2      -2
       2      -3      -4       0      12
       1      -2       2       3       2       0
       2       2       2       6      -8       6      -2
       1       2       3       3      -1      -1       3       0
      -1       2       7       2       5       0     -11      -5      -3
       1       1      -4      -4      -1       1      -4       0       1       2
       3      -2       0      -1       4      -2      -1      -2       3       3      -3
       1       4       1       0      -1       3       2       2       2      -4       0       0
       4      -5      -1      -1       3      -1      -3       1       3       1       8       1      -9
      -1       5       1      -3      -1      -6      -4      -1       0       5       3       0       0      -3
       2       1       0       3      -1       1       1       0       2       2       0       4     -17       4      -1
       0       2       5       3      -5       0       2       4       1      -1      -1       0      -3      -2       5     -10
       1       0       1       3       2       3       2       0       5       0      -3      -2       3       3      -1       4       0
      -4      -5      -3      -4       1      -1      -1       0       2       2       4       3       0      11       2       0       3       5
       1       3      -3       0       0       2      -2       1       3       3       3       0       4       0      -3       2       1     -12      -4
      -1      -4      -1      -2       7       2      -3      -3       0       4       6       0       3       5      -1       1       0       2       3      -1
//
H RUSR970102
D Substitution matrix based on structural alignments of remote homolous proteins
  (Russell et al., 1997)
R PMID:919941
A Russell, R.B., Saqi, M.A.S., Sayle, R.A., Bates, P.A. and Sternberg, M.J.E.
T Recognition of analogous and homologous protein folds: Analysis of sequence and
  structure conservation
J Journal of Molecular Biology 269, 423-439 (1997)
M rows = ARNDCQEGHILKMFPSTWYV, cols = ARNDCQEGHILKMFPSTWYV
       0
       0       4
       0       0       3
      -1       0       5       5
       2      -1       0      -1      13
      -1       3       2       3      -6       4
       0       2       0       5      -4       2       3
       1       0       1       1      -1       0      -1       6
      -2       2       4       2       1       4       3      -1      11
       0       0      -8      -7       1      -3      -3      -4      -4       1
       0      -2      -2      -7       2      -5      -2      -4       0       7       2
       1       6       1       1       0       4       4       0       1      -6      -4       2
       0       0      -3      -6       1       0      -3      -3       1       5       6      -1       3
       0      -3      -1      -6       3      -2      -5      -6       0       4       4      -4       4       5
       0      -1       2       1      -1       0       2       0       1      -2      -5       0      -3      -1       7
       2       0       3       2      -1       4       1       0      -4      -4      -2       0      -2       0       2       0
       0       0       4       1      -2      -2       0       0       1       0       0       2       2      -2       1       4       0
      -1       2       0      -5       2      -3      -2      -2       0       3       0      -2       3       4      -2       1      -4      16
       0       2       0      -2       4       1      -1      -1       2       0       0       0       1       7       0       0      -1       8       3
       1      -1      -3      -3       2      -1      -2      -2      -3       7       3      -2       3       3       0      -1       0      -2       1       0
//
H RUSR970103
D Substitution matrix based on structural alignments of analogous and remote homolous
  proteins (Russell et al., 1997)
R PMID:9199410
A Russell, R.B., Saqi, M.A.S., Sayle, R.A., Bates, P.A. and Sternberg, M.J.E.
T Recognition of analogous and homologous protein folds: Analysis of sequence and
  structure conservation
J Journal of Molecular Biology 269, 423-439 (1997)
M rows = ARNDCQEGHILKMFPSTWYV, cols = ARNDCQEGHILKMFPSTWYV
      -2
       1       0
       0       0       0
      -1       0       1       0
       2      -4      -1       0      12
       0       1       3       3      -4       0
       1       2       0       4      -8       4       0
       0       1       2       2       0       0       1       1
       0       3       3       3       2       0      -1      -3       1
       1       1      -7      -3      -4       0      -3      -1      -1       0
       2      -2       0      -3       2      -2       0      -2       2       5       0
       1       3       0       2       2       4       3       1       3      -5      -2      -1
       2       0      -3      -2       1       0      -1       0       3       4       6       0      -5
       0      -1       1      -4       3      -3      -5      -3       0       4       4      -1       0       0
       0       0       1       3       0       0       1       1       2       0      -2       1       0       1       0
       0       0       4       2      -3       1       2       0      -1      -3       0       0      -4       0       5      -3
       0       0       3       2       0       0       1       0       3       0      -1       1       2       0       1       3      -2
       0       0      -1      -5       2      -1      -3      -1       0       4       1       0       3       5       2       2       0       7
       0       3       0      -1       1       0      -1       0       1       2       0       0       1       5      -1       0       0       4      -1
       0       0       0      -1       5       0      -2      -1      -1       5       4       0       1       3      -1       0       0       0       2      -2
//
H OGAK980101
D Substitution matrix derived from structural alignments by maximizing entropy
  (Ogata et al., 1998)
R PMID:10522237
A Ogata, K., Ohya, M. and Umeyama, H.
T Amino acid similarity matrix for homology modeling derived from structural
  alignment and optimized by the Monte Carlo method
J Journal of Molecular Graphics and Modelling 16, 178-254 (1998)
M rows = ARNDCQEGHILKMFPSTWYV, cols = ARNDCQEGHILKMFPSTWYV
    -4.8
    -7.0    -6.2
    -7.1    -7.3    -4.8
    -6.9    -7.3    -6.3    -5.0
    -7.7    -8.3    -8.6    -8.3    -3.2
    -7.0    -7.5    -7.1    -7.3    -8.3    -6.5
    -6.7    -7.5    -6.5    -6.4   -10.2    -6.8    -5.4
    -5.8    -7.5    -6.8    -6.3    -7.5    -7.6    -7.4    -4.2
    -7.7    -8.1    -6.8    -8.1    -9.3    -7.7    -7.8    -7.7    -6.1
    -7.1    -7.7    -7.6    -8.3    -9.0    -7.9    -8.3    -8.0    -8.2    -5.5
    -6.7    -7.9    -7.7    -7.1    -7.7    -7.4    -7.4    -8.0    -8.1    -5.5    -4.0
    -6.7    -6.6    -6.8    -6.9    -8.5    -6.7    -6.7    -6.8    -7.6    -8.1    -7.2    -5.5
    -8.0    -7.8    -7.4    -8.2    -8.7    -8.5    -8.1    -8.2    -9.7    -7.4    -7.0    -8.2    -6.7
    -7.9    -8.1    -8.2    -9.5    -8.9    -8.6    -8.2    -8.1    -8.2    -7.2    -6.6    -8.8    -8.5    -5.7
    -6.8    -7.9    -8.0    -7.3    -8.3    -8.1    -7.8    -7.2    -7.5    -7.2    -6.6    -7.5    -8.8    -8.8    -5.7
    -5.6    -6.9    -6.5    -5.7    -8.2    -7.0    -6.6    -6.3    -7.0    -7.2    -6.4    -6.6    -7.5    -8.3    -6.8    -4.6
    -6.2    -6.8    -6.4    -6.5    -7.5    -7.0    -6.8    -6.7    -8.0    -7.1    -6.2    -6.3    -7.3    -7.7    -6.7    -5.5    -5.0
    -9.0    -9.4    -8.6    -9.8   -12.0    -8.3    -7.9    -7.2    -9.7    -7.7    -6.8    -9.5    -7.2    -6.9   -10.4    -7.6    -7.6    -5.0
    -7.5    -8.4    -7.0    -7.2   -10.6    -7.3    -7.5    -7.5    -6.8    -7.4    -6.6    -7.3    -7.9    -6.0    -8.1    -7.3    -6.8    -6.5    -4.7
    -5.9    -7.4    -7.2    -7.1    -8.1    -7.5    -7.3    -7.3    -7.5    -5.7    -5.8    -6.7    -7.2    -7.1    -7.5    -6.8    -6.2    -7.8    -7.2    -4.8
//
H KANM000101
D Substitution matrix (OPTIMA) derived by maximizing discrimination between
  homologs and non-homologs (Kann et al., 2000)
R PMID:11056037
A Kann, M., Qian, B. and Goldstein, R.A.
T Optimization of a new score function for the detection of remote homologs
J Proteins: Structure, Function, and Genetics 41, 498-503 (2000)
M rows = ARNDCQEGHILKMFPSTWYV, cols = ARNDCQEGHILKMFPSTWYV
      36
      -9      56
     -19       4      59
     -20     -18      18      65
       6     -29     -30     -30      99
      -3      12       2       2     -30      46
     -10       3       3      20     -39      19      40
       4     -18       7     -10     -29     -20     -23      67
     -19       3      12      -7     -29       3       2     -18      86
      -5     -28     -32     -34      -6     -30     -33     -41     -28      35
      -7     -20     -32     -43      -6     -23     -31     -42     -27      28      32
     -10      31       1      -4     -29      15      14     -18      -7     -31     -21      37
      -9     -10     -19     -30      -8       1     -21     -30     -19      12      24     -12      51
     -19     -30     -29     -33     -18     -29     -32     -32      -8       8      17     -29       2      57
      -5     -18     -17      -7     -30     -11      -7     -18     -18     -30     -33     -10     -21     -39      74
      12     -11      10       4     -10       0      -1       2      -9     -20     -22       3     -10     -19      -8      36
       0      -8       0     -10      -7      -7      -6     -17     -20      -8     -13      -8      -7     -18     -11      18      48
     -29     -29     -39     -40     -18     -19     -29     -19     -18     -28     -15     -30      -8      14     -38     -29     -19     110
     -19     -15     -19     -20     -18      -9     -21     -29      20      -8      -2     -17      -9      37     -28     -19     -17      22      69
       6     -32     -31     -31      -6     -19     -28     -30     -29      35      18     -23      10       0     -18     -22       6     -28      -9      38
//
H NGPC000101
D Substitution matrix (PHAT) built from hydrophobic and transmembrane regions
  of the Blocks database (Ng et al., 2000)
R PMID:11108698
A Ng, P.C., Henikoff, J.G. and Henikoff, S.
T PHAT: a transmembrane-specific substitution matrix
J Bioinformatics 16, 760-766 (2000)
M rows = ARNDCQEGHILKMFPSTWYV, cols = ARNDCQEGHILKMFPSTWYV
       5
      -6       9
      -2      -3      11
      -5      -7       2      12
       1      -8      -2      -7       7
      -3      -2       2       0      -5       9
      -5      -6       0       6      -7       1      12
       1      -5      -1      -2      -2      -2      -3       9
      -3      -4       4      -1      -7       2      -1      -4      11
       0      -6      -3      -5      -3      -3      -5      -2      -5       5
      -1      -6      -3      -5      -2      -3      -5      -2      -4       2       4
      -7      -1      -2      -5     -10      -1      -4      -5      -5      -7      -7       5
      -1      -6      -2      -5      -2      -1      -5      -1      -4       3       2      -6       6
      -1      -7      -1      -5       0      -2      -5      -2      -2       0       1      -7       0       6
      -3      -7      -4      -5      -8      -3      -5      -3      -6      -4      -5      -4      -5      -5      13
       2      -6       1      -4       1      -1      -3       1      -2      -2      -2      -5      -2      -2      -3       6
       0      -6      -1      -5      -1      -3      -5      -1      -4      -1      -1      -6       0      -2      -4       1       3
      -4      -7      -5      -7      -4       1      -7      -5      -3      -4      -3      -8      -4       0      -6      -5      -7      11
      -3      -6       2      -4      -1       0      -2      -3       3      -3      -2      -4      -2       4      -5      -2      -3       1      11
       1      -7      -3      -5      -2      -3      -5      -2      -5       3       1      -8       1      -1      -4      -2       0      -4      -3       4
//
H MUET010101
D Non-symmetric substitution matrix (SLIM) for detection of homologous
  transmembrane proteins (Mueller et al., 2001)
R PMID:11473008
A Mueller, T., Rahmann, S. and Rehmsmeier, M.
T Non-symmetric score matrices and the detection of homologous transmembrane
  proteins
J Bioinformatics 17 Suppl 1, S182-S189 (2001)
M rows = ARNDCQEGHILKMFPSTWYV, cols = ARNDCQEGHILKMFPSTWYV
     5.0
    -5.5    10.0
    -3.0    -4.5     8.0
    -6.5    -9.5    -0.5     9.0
     2.5    -5.0    -2.5    -7.5    11.0
    -4.0    -2.5    -1.0    -2.5    -3.5     7.0
    -7.0    -9.0    -4.5     2.0    -7.0    -2.5     7.0
     0.5    -5.5    -3.0    -4.5    -1.5    -3.5    -6.5     7.0
    -3.0    -4.5     2.5    -3.5    -5.0    -0.5    -3.0    -5.5    10.0
     0.0    -5.5    -4.0    -6.5    -0.5    -3.5    -7.0    -2.5    -4.0     6.0
     0.0    -4.5    -3.5    -6.0     1.0    -3.5    -7.0    -2.0    -4.0     3.5     5.0
    -5.5    -0.5    -3.5    -5.0    -7.0    -2.0    -7.5    -4.5    -5.5    -5.5    -6.0     6.0
     0.0    -4.0    -3.0    -6.0     1.0    -1.5    -6.0    -1.5    -4.0     4.0     4.0    -5.5     7.0
     0.0    -5.5    -2.0    -5.5     2.5    -2.0    -5.5    -1.0    -1.0     1.5     2.5    -5.5     2.5     8.0
    -4.0    -8.0    -6.0    -7.0    -9.0    -6.0    -7.0    -4.5    -8.0    -4.0    -5.0    -4.5    -5.0    -4.5    11.0
     2.0    -6.0     0.5    -5.5     3.0    -2.5    -5.0     0.5    -2.5    -1.5    -1.5    -5.0    -1.0    -0.5    -4.0     6.0
     1.5    -5.0    -1.5    -5.5     1.0    -3.5    -6.5    -1.5    -3.5     0.5     0.5    -5.0     1.5     0.0    -3.5     1.5     4.0
    -2.5    -4.5    -4.0    -6.5    -0.5     1.0    -6.0    -4.0    -1.0    -1.5    -0.5    -5.5    -0.5     3.5    -4.5    -3.0    -4.5    15.0
    -3.5    -5.5     0.0    -5.5     0.5    -2.0    -5.5    -3.5     2.5    -2.5    -1.5    -3.5    -1.5     5.0    -5.5    -2.0    -2.5     2.0    11.0
     1.5    -6.0    -4.5    -6.0     1.0    -3.5    -6.5    -2.5    -4.5     4.5     2.5    -7.0     2.5     1.0    -4.0    -1.0     1.0    -2.0    -2.5     5.0
//
H MUET020101
D Substitution matrix (VTML160) obtained by maximum likelihood estimation
  (Mueller et al., 2002)
R PMID:11752185
A Mueller, T., Spang, R. and Vingron, M.
T Estimating amino acid substitution models: A comparison of Dayhoff's
  estimator, the resolvent approach and a maximum likelihood method
J Molecular Biology and Evolution 19, 8-13 (2002)
M rows = ARNDCQEGHILKMFPSTWYV, cols = ARNDCQEGHILKMFPSTWYV
       5
      -2       7
      -1       0       7
      -1      -3       3       7
       1      -3      -3      -5      13
      -1       2       0       1      -4       6
      -1      -1       0       3      -5       2       6
       0      -3       0      -1      -2      -3      -2       8
      -2       1       1       0      -2       2      -1      -3       9
      -1      -4      -4      -6      -1      -4      -5      -7      -4       6
      -2      -3      -4      -6      -4      -2      -4      -6      -3       3       6
      -1       4       0       0      -4       2       1      -2       0      -4      -3       5
      -1      -2      -3      -5      -1      -1      -3      -5      -3       2       4      -2       8
      -3      -5      -5      -7      -4      -4      -6      -6       0       0       2      -5       1       9
       0      -2      -2      -1      -3      -1      -1      -3      -2      -4      -3      -1      -4      -5       9
       1      -1       1       0       1       0       0       0      -1      -3      -3      -1      -3      -3       0       4
       1      -1       0      -1       0      -1      -1      -2      -1      -1      -2      -1      -1      -3      -1       2       5
      -5      -4      -5      -7      -7      -6      -7      -5      -1      -2      -1      -5      -4       3      -5      -4      -6      16
      -3      -3      -2      -5      -1      -4      -3      -5       3      -2      -1      -3      -2       6      -6      -2      -3       4      10
       0      -4      -4      -4       1      -3      -3      -5      -3       4       2      -3       1      -1      -3      -2       0      -5      -3       5
//
H MUET020102
D Substitution matrix (VTML250) obtained by maximum likelihood estimation
  (Mueller et al., 2002)
R 11752185
A Mueller, T., Spang, R. and Vingron, M.
T Estimating amino acid substitution models: A comparison of Dayhoff's
  estimator, the resolvent approach and a maximum likelihood method
J Molecular Biology and Evolution 19, 8-13 (2002)
M rows = ARNDCQEGHILKMFPSTWYV, cols = ARNDCQEGHILKMFPSTWYV
       2
      -1       5
       0       0       4
       0      -1       2       5
       1      -2      -1      -3      11
       0       2       1       1      -2       3
       0       0       1       3      -3       2       4
       1      -1       0       0      -1      -1      -1       7
      -1       1       1       0      -1       1       0      -1       6
      -1      -2      -3      -4       0      -2      -3      -4      -2       4
      -1      -2      -3      -4      -2      -2      -3      -4      -2       3       4
      -1       3       1       0      -2       2       1      -1       0      -2      -2       3
      -1      -1      -2      -3       0      -1      -2      -3      -2       2       3      -1       4
      -2      -3      -3      -5      -2      -2      -4      -4       0       1       2      -3       1       7
       0      -1      -1       0      -2       0       0      -1      -1      -3      -2       0      -2      -3       7
       1       0       1       0       1       0       0       0       0      -2      -2       0      -1      -2       0       2
       1      -1       0       0       0       0       0      -1       0       0      -1       0       0      -2       0       1       3
      -3      -3      -4      -5      -4      -4      -5      -4       0      -1       0      -3      -2       3      -3      -3      -4      14
      -2      -2      -1      -3       0      -2      -2      -4       2      -1       0      -2      -1       5      -4      -1      -2       4       8
       0      -2      -2      -3       1      -2      -2      -3      -2       3       2      -2       2       0      -2      -1       0      -3      -1       3
//
H CROG050101
D Substitution matrix computed from the Dirichlet Mixture Model
  (Crooks-Brenner, 2005)
R PMID:15531614
A Crooks, G.E. and Brenner, S.E.
T An alternative model of amino acid replacement
J Bioinformatics 21, 975-980 (2005)
M rows = ARNDCQEGHILKMFPSTWYV, cols = ARNDCQEGHILKMFPSTWYV
       4
      -2       6
      -2      -1       7
      -2      -1       1       7
       0      -4      -3      -4      12
      -1       1       0       0      -3       6
      -1       0       0       1      -4       1       5
      -1      -3      -1      -1      -3      -2      -2       7
      -2       0       0      -1      -3       0      -1      -2       9
      -2      -3      -5      -6      -1      -3      -4      -6      -3       5
      -2      -3      -4      -5      -2      -3      -4      -5      -3       2       5
      -2       2       0       0      -4       1       1      -2      -1      -4      -3       5
      -1      -2      -3      -4      -1      -2      -3      -4      -2       1       2      -2       7
      -2      -3      -4      -5      -2      -3      -4      -5      -1       0       1      -4       1       7
      -1      -2      -2      -1      -3      -1      -1      -2      -2      -4      -3      -1      -3      -3       8
       0      -1       0       0      -2       0      -1      -1      -1      -4      -3      -1      -2      -3      -1       4
      -1      -1      -1      -1      -1      -1      -1      -2      -1      -2      -2      -1      -1      -2      -2       1       5
      -3      -2      -3      -4      -2      -2      -3      -4       0      -1      -1      -3       0       3      -3      -3      -2      12
      -2      -2      -2      -3      -2      -2      -3      -4       0      -1      -1      -3       0       3      -3      -2      -2       3       8
      -1      -3      -4      -5       0      -3      -4      -5      -3       3       1      -3       1       0      -3      -3      -1      -2      -2       5
//