diff --git a/scripts/aa_index/aa_index.R b/scripts/aa_index_scripts/aa_index.R similarity index 100% rename from scripts/aa_index/aa_index.R rename to scripts/aa_index_scripts/aa_index.R diff --git a/scripts/aa_index_scripts/aaindex.zip b/scripts/aa_index_scripts/aaindex.zip new file mode 100644 index 0000000..9f992a9 Binary files /dev/null and b/scripts/aa_index_scripts/aaindex.zip differ diff --git a/scripts/aa_index_scripts/aaindex/data/aaindex2 b/scripts/aa_index_scripts/aaindex/data/aaindex2 new file mode 100644 index 0000000..8cf88d7 --- /dev/null +++ b/scripts/aa_index_scripts/aaindex/data/aaindex2 @@ -0,0 +1,2818 @@ +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 + 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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 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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 rows = 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 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Functional forms and parameters of long-range side-chain interaction + potentials from protein crystal data. +J J. Comp. 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PMID:8627632 +A Park, B. and Levitt, M. +T Energy functions that discriminate X-ray and near-native folds + from well-constructed decoys +J J. 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Mol. Biol. 258, 367-392 (1996) +* (Glu is not available) +M rows = ARNDCQEGHILKMFPSTWYV, cols = ARNDCQEGHILKMFPSTWYV + -2.9 + -2.4 -2.9 + -2.8 -3.2 -3.6 + -2.6 -3.7 -3.3 -2.6 + -3.1 -2.6 -3.2 -2.9 -6.1 + -2.7 -2.9 -3.2 -2.7 -2.9 -2.6 + -1.9 -3.2 -2.8 -2.0 -2.4 -2.2 -1.5 + NA NA NA NA NA NA NA NA + -2.6 -2.9 -3.2 -3.3 -3.3 -2.5 -2.8 NA -3.5 + -3.9 -3.3 -3.2 -2.9 -4.2 -3.2 -2.7 NA -3.4 -4.9 + -3.7 -3.0 -3.0 -2.7 -4.0 -3.1 -2.4 NA -3.1 -4.6 -4.3 + -1.9 -2.0 -3.0 -3.5 -2.4 -2.7 -3.2 NA -2.2 -2.9 -2.5 -1.7 + -3.8 -3.1 -3.3 -2.7 -4.2 -3.3 -2.7 NA -3.5 -4.7 -4.4 -2.9 -4.8 + -3.7 -3.0 -3.2 -2.7 -4.1 -3.0 -2.4 NA -3.3 -4.5 -4.2 -2.8 -4.6 -4.3 + -2.3 -2.4 -2.7 -2.3 -2.8 -2.5 -1.8 NA -2.6 -3.0 -2.8 -1.8 -3.4 -3.1 -2.2 + -2.4 -2.6 -2.8 -2.8 -3.0 -2.3 -2.3 NA -2.7 -3.0 -2.6 -2.3 -3.0 -2.8 -2.2 -2.4 + -3.2 -3.1 -3.4 -3.2 -3.5 -3.1 -2.7 NA -3.2 -3.8 -3.3 -2.8 -3.8 -3.4 -2.8 -2.9 -3.5 + -3.8 -3.5 -3.5 -3.2 -4.3 -3.3 -2.8 NA -3.6 -4.7 -4.4 -3.3 -4.8 -4.4 -3.7 -3.1 -3.7 -4.7 + -3.7 -3.6 -3.5 -3.5 -3.8 -3.4 -3.0 NA -3.7 -4.4 -4.1 -3.5 -4.4 -4.1 -3.5 -3.1 -3.6 -4.3 -4.1 + -4.1 -3.5 -3.5 -2.8 -4.3 -3.4 -2.8 NA -3.5 -5.0 -4.7 -3.1 -4.7 -4.6 -3.2 -3.1 -3.9 -4.8 -4.5 -5.1 +// +H KOLA930101 +D Statistical potential derived by the quasichemical approximation +A Kolinski, A., Godzik, A. and Skolnick, J. +T A general method for the prediction of the three dimensional structure + and folding pathway of globular proteins: Application to designed helical + proteins +J J. Chem. 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Comput. Aided Mol. 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Natl. Acad. Sci. 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Natl. Acad. Sci. USA 97, 2550-2555 (2000) +M rows = ARNDCQEGHILKMFPSTWYV, cols = ARNDCQEGHILKMFPSTWYV + 0.12 + 0.56 1.18 + 0.59 0.83 0.83 + 0.65 0.33 0.61 1.15 + -0.74 -0.25 -0.07 -0.12 -2.42 + 0.70 0.94 0.87 0.96 -0.05 1.22 + 1.32 0.54 1.09 1.48 0.20 1.11 2.18 + 0.11 0.65 0.79 0.75 -0.56 0.73 1.16 0.35 + 0.35 0.47 0.91 0.29 -0.83 0.83 0.74 0.53 0.28 + -0.45 0.05 0.40 0.47 -1.27 0.24 0.70 0.01 -0.21 -1.04 + -0.25 0.26 0.37 0.57 -1.25 0.38 0.82 0.13 -0.03 -1.15 -1.04 + 1.06 1.65 1.11 0.58 0.76 1.29 0.93 1.08 1.23 0.48 0.78 2.23 + 0.29 0.58 0.68 0.75 -0.74 0.65 1.08 0.54 0.19 -0.52 -0.68 1.15 -0.12 + -0.41 0.24 0.46 0.38 -1.44 0.39 0.55 0.09 -0.28 -1.09 -1.05 0.74 -0.60 -1.09 + 0.48 0.82 1.09 1.26 -0.23 1.09 1.25 0.74 0.59 0.14 0.10 1.59 0.54 -0.04 1.11 + 0.45 0.55 0.81 0.54 -0.47 0.75 0.87 0.61 0.46 0.09 0.01 1.24 0.56 0.17 0.94 0.87 + 0.30 0.80 0.54 0.51 -0.37 0.81 0.81 0.38 0.31 -0.28 -0.05 1.10 0.46 0.08 0.67 0.54 0.69 + -0.28 -0.04 0.13 0.43 -0.63 -0.01 0.44 -0.17 -0.44 -1.28 -0.98 0.23 -0.50 -1.02 -0.33 0.14 -0.19 -0.46 + -0.07 0.22 0.40 0.38 -0.58 0.09 0.47 0.28 -0.18 -0.74 -0.56 0.62 -0.26 -0.63 0.04 0.23 0.27 -0.87 -0.18 + -0.18 0.43 0.54 0.59 -1.22 0.23 0.74 0.04 0.09 -0.90 -0.93 0.81 -0.31 -0.77 0.17 0.20 -0.10 -0.57 -0.38 -0.31 +// diff --git a/scripts/aa_index_scripts/aaindex/data/aaindex3.p b/scripts/aa_index_scripts/aaindex/data/aaindex3.p new file mode 100644 index 0000000..710210b Binary files /dev/null and b/scripts/aa_index_scripts/aaindex/data/aaindex3.p differ diff --git a/scripts/aa_index_scripts/aaindex/data/parse_aaindex.py b/scripts/aa_index_scripts/aaindex/data/parse_aaindex.py new file mode 100644 index 0000000..89efe65 --- /dev/null +++ b/scripts/aa_index_scripts/aaindex/data/parse_aaindex.py @@ -0,0 +1,90 @@ +from collections import defaultdict + +import os +import pickle + +DATA_FOLDER = "/home/chmrodrigues/Documents/ppi2/reverse_mutations/data/aaindex" + +def main(): + + aaindex2_file = os.path.join(DATA_FOLDER,"aaindex2") + aaindex3_file = os.path.join(DATA_FOLDER,"aaindex3") + + lines_index2 = ' '.join([item for item in open(aaindex2_file,'r').readlines()]) + lines_index3 = ' '.join([item for item in open(aaindex3_file,'r').readlines()]) + + attrs_index2 = [item for item in lines_index2.split('//\n') if len(item) != 0] + attrs_index3 = [item for item in lines_index3.split('//\n') if len(item) != 0] + + attr_name = str() + all_matrices = dict() + for line in attrs_index2: + attr_elements = line.split('\n') + + attr_name = [item for item in attr_elements if item.strip().startswith("H ")][0].split()[-1] + rows_columns_index = [attr_elements.index(item) for item in attr_elements if item.startswith(" M rows =")][0] + + rows = attr_elements[rows_columns_index].split()[3].replace(",","") + columns = attr_elements[rows_columns_index].split()[-1] + + attr_dict = dict() + for row in rows: + attr_dict[row] = dict() + for col in columns: + attr_dict[row][col] = None + + for i in range(rows_columns_index+1,len(attr_elements)): + values = attr_elements[i].split() + try: + row = rows[i-(rows_columns_index+1)] + for idx,value in enumerate(values): + col = columns[idx] + try: + attr_dict[row][col] = float(value) + except ValueError: + attr_dict[row][col] = value + except IndexError: + pass + + all_matrices[attr_name] = attr_dict + print(len(all_matrices)) + pickle.dump(all_matrices, open('index2.p','wb'),protocol=2) + + attr_name = str() + all_matrices = dict() + for line in attrs_index3: + attr_elements = line.split('\n') + + attr_name = [item for item in attr_elements if item.strip().startswith("H ")][0].split()[-1] + rows_columns_index = [attr_elements.index(item) for item in attr_elements if item.startswith(" M rows =")][0] + + rows = attr_elements[rows_columns_index].split()[3].replace(",","") + columns = attr_elements[rows_columns_index].split()[-1] + + attr_dict = dict() + for row in rows: + attr_dict[row] = dict() + for col in columns: + attr_dict[row][col] = None + + for i in range(rows_columns_index+1,len(attr_elements)): + values = attr_elements[i].split() + try: + row = rows[i-(rows_columns_index+1)] + for idx,value in enumerate(values): + col = columns[idx] + try: + attr_dict[row][col] = float(value) + except ValueError: + attr_dict[row][col] = value + except IndexError: + pass + + all_matrices[attr_name] = attr_dict + pickle.dump(all_matrices, open('index3.p','wb'),protocol=2) + print(len(all_matrices)) + + return True + +if __name__ == "__main__": + main() diff --git a/scripts/aa_index_scripts/aaindex/get_scores.py b/scripts/aa_index_scripts/aaindex/get_scores.py new file mode 100644 index 0000000..9b104a9 --- /dev/null +++ b/scripts/aa_index_scripts/aaindex/get_scores.py @@ -0,0 +1,161 @@ +""" + RSA <= 0.2 Buried (Inaccessible) + RSA > 0.2 Exposed (Accessible) + + SST = [H,I,G] - Helix + SST = [B,E] - Beta + SST = [T] - Turn + SST = [S,-] - Coil +""" +from Bio.PDB import PDBParser, DSSP +import pickle +import os +import sys +import warnings + +warnings.filterwarnings("ignore") + +CURRENT_FOLDER = '/home/local/BHRI/sportelli/Desktop/Important_Code/structural/aaindex' +DATA_FOLDER = os.path.join(CURRENT_FOLDER,'data') + +RSA_SST_DEPENDENT = { + 'exposed_helix' : 'KOSJ950101', + 'exposed_beta' : 'KOSJ950102', + 'exposed_turn' : 'KOSJ950103', + 'exposed_coil' : 'KOSJ950104', + 'buried_helix' : 'KOSJ950105', + 'buried_beta' : 'KOSJ950106', + 'buried_turn' : 'KOSJ950107', + 'buried_coil' : 'KOSJ950108', +} + +SST_DEPENDENT = { + 'helix' : 'KOSJ950109', + 'beta' : 'KOSJ950110', + 'turn' : 'KOSJ950111', + 'coil' : 'KOSJ950112', +} + +RSA_DEPENDENT1 = { + 'exposed' : 'KOSJ950113', + 'buried' : 'KOSJ950114', +} + +RSA_DEPENDENT2 = { + 'exposed' : 'OVEJ920104', + 'buried' : 'OVEJ920105', +} + +def get_environment(pdb_file, chain, position, insertion_code=' '): + parser = PDBParser() + structure = parser.get_structure(pdb_file, pdb_file) + model = structure[0] + + dssp = DSSP(model, pdb_file) + dssp_key = [item for item in dssp.keys() if item[0] == chain and item[1][1] == int(position) and item[1][2] == insertion_code] + + dssp_key = dssp_key[0] + sst = dssp[dssp_key][2] + rsa = float(dssp[dssp_key][3]) + + return{'sst':sst, 'rsa':rsa} + +def main(): + """ + READ IMPUT + """ + pdb_file = sys.argv[1] + chain_id = sys.argv[2] + mutation_code = sys.argv[3] + + aa_from = mutation_code[0] + aa_to = mutation_code[-1] + position = mutation_code[1:-1] + insertion_code = ' ' + if not position[-1].isdigit(): + insertion_code = position[-1] + position = position[:-1] + + """ + READ DATABASES + index2 - Amino acid substitution indexes + index3 - Statistical protein contact potentials + """ + index2 = pickle.load(open('{}/aaindex2.p'.format(DATA_FOLDER),'rb')) + index3 = pickle.load(open('{}/aaindex3.p'.format(DATA_FOLDER),'rb')) + + """ + LOOP THROUGH TABLES AND EXTRACT VALUES + """ + results_index2 = dict() + results_index3 = dict() + for key in index2.keys(): + if index2[key][aa_from][aa_to] != None: + results_index2[key] = index2[key][aa_from][aa_to] + else: + results_index2[key] = index2[key][aa_to][aa_from] + + for key in index3.keys(): + if index3[key][aa_from][aa_to] != None: + results_index3[key] = index3[key][aa_from][aa_to] + else: + results_index3[key] = index3[key][aa_to][aa_from] + + """ + GET ENVIRONMENT CHARACTERISTICS + """ + environment = get_environment(pdb_file, chain_id, position, insertion_code) + + buried = 'buried' + sst = str() + if environment['rsa'] <= 0.2: + buried = 'exposed' + + if environment['sst'] in ['H','I','G']: + sst = 'helix' + elif environment['sst'] in ['B','E']: + sst = 'beta' + elif environment['sst'] in ['T']: + sst = 'turn' + else: + sst = 'coil' + + results_index2['KOSJ950100_RSA_SST'] = results_index2[RSA_SST_DEPENDENT['{}_{}'.format(buried,sst)]] + results_index2['KOSJ950100_SST'] = results_index2[SST_DEPENDENT[sst]] + results_index2['KOSJ950110_RSA'] = results_index2[RSA_DEPENDENT1[buried]] + results_index2['OVEJ920100_RSA'] = results_index2[RSA_DEPENDENT2[buried]] + + for value in RSA_SST_DEPENDENT.values(): + results_index2.pop(value) + for value in SST_DEPENDENT.values(): + results_index2.pop(value) + for value in RSA_DEPENDENT1.values(): + results_index2.pop(value) + for value in RSA_DEPENDENT2.values(): + results_index2.pop(value) + + """ + PRINT RESULTS + """ + output_dict = dict() + output_dict.update(results_index2) + output_dict.update(results_index3) + + keys = list(output_dict.keys()) + keys.sort() + values = [str(output_dict[item]) for item in keys] + + # print(",".join(keys)) + print(",".join(values)) + + return True + + +if __name__ == "__main__": + + if len(sys.argv) != 4: + print("Error on parsing argument list") + print("Please provide a one letter code for wild-type and mutant residues") + print("Eg.: python get_scores.py pdb_file chain_id mutation_code") + sys.exit(1) + main() diff --git a/scripts/aa_index/run_aa_index.R b/scripts/aa_index_scripts/run_aa_index.R similarity index 100% rename from scripts/aa_index/run_aa_index.R rename to scripts/aa_index_scripts/run_aa_index.R