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 //