# TARGET T0311 # Using neural net dunbrack-40pc-3157-t06-IDGaaH13-3-13-7-13-9-13-11-pb-seeded.net # This is a 4-layer network, with # window units # 3 13 # 7 13 # 9 13 # 11 16 (1 pb ) # The input amino acid frequencies were determined from # alignment /projects/compbio/experiments/protein-predict/casp7/T0311/T0311.t04-thin90.a2m.gz # with weighted counts, using HenikoffWeight(1.3 bits/column, 1) # The weighting was determined by the posterior distribution # after regularizing with /projects/compbio/lib/recode3.20comp. # Counts were regularized to probabilities using # /projects/compbio/lib/recode3.20comp # Total sequence weight for alignment was 61.1882 # Pos AA A B C D E F G H I J K L M N O P 10N 1S 5N 5N 5N 5N 5N 5N 5N 5N 5N 5N 5N 5N 5N 5N 5N 5N 1 M 0.100 0.028 0.196 0.370 0.020 0.053 0.026 0.005 0.019 0.015 0.018 0.025 0.071 0.007 0.004 0.043 2 K 0.057 0.066 0.272 0.336 0.017 0.103 0.009 0.019 0.003 0.003 0.022 0.020 0.054 0.002 0.008 0.008 3 M 0.012 0.042 0.064 0.297 0.116 0.188 0.028 0.015 0.013 0.014 0.093 0.026 0.047 0.027 0.003 0.015 4 A 0.028 0.236 0.074 0.369 0.018 0.037 0.015 0.056 0.011 0.004 0.030 0.046 0.037 0.006 0.026 0.008 5 N 0.020 0.072 0.130 0.396 0.014 0.041 0.026 0.015 0.069 0.032 0.018 0.035 0.046 0.007 0.013 0.066 6 H 0.152 0.040 0.241 0.295 0.019 0.063 0.020 0.012 0.014 0.009 0.029 0.016 0.042 0.003 0.008 0.038 7 P 0.049 0.102 0.256 0.470 0.009 0.027 0.003 0.006 0.006 0.008 0.014 0.018 0.018 0.001 0.002 0.011 8 R 0.013 0.010 0.021 0.080 0.270 0.471 0.039 0.003 0.001 0.014 0.014 0.032 0.021 0.010 0.001 0.002 9 P 0.002 0.033 0.008 0.031 0.001 0.088 0.001 0.301 0.001 0.001 0.465 0.015 0.039 0.001 0.015 0.001 10 G 0.002 0.009 0.003 0.019 0.001 0.021 0.001 0.001 0.083 0.058 0.147 0.560 0.088 0.001 0.001 0.009 11 D 0.052 0.008 0.011 0.023 0.001 0.006 0.001 0.001 0.001 0.001 0.068 0.344 0.485 0.001 0.001 0.001 12 I 0.001 0.001 0.016 0.010 0.001 0.040 0.001 0.001 0.001 0.001 0.015 0.053 0.860 0.001 0.001 0.002 13 I 0.001 0.007 0.001 0.004 0.001 0.014 0.001 0.001 0.001 0.001 0.004 0.032 0.937 0.001 0.001 0.001 14 Q 0.001 0.001 0.001 0.006 0.001 0.005 0.001 0.001 0.001 0.001 0.011 0.010 0.964 0.001 0.001 0.001 15 E 0.001 0.002 0.001 0.004 0.001 0.001 0.001 0.001 0.001 0.001 0.005 0.012 0.969 0.001 0.003 0.001 16 S 0.001 0.003 0.006 0.005 0.001 0.002 0.005 0.001 0.001 0.001 0.001 0.005 0.859 0.033 0.004 0.077 17 L 0.002 0.005 0.049 0.012 0.001 0.002 0.027 0.001 0.001 0.001 0.001 0.002 0.868 0.002 0.018 0.011 18 D 0.002 0.002 0.016 0.003 0.003 0.081 0.012 0.001 0.001 0.001 0.005 0.005 0.836 0.009 0.004 0.021 19 E 0.001 0.004 0.001 0.001 0.010 0.001 0.039 0.001 0.001 0.001 0.053 0.001 0.029 0.854 0.001 0.003 20 L 0.001 0.008 0.003 0.001 0.001 0.001 0.003 0.025 0.001 0.001 0.002 0.037 0.016 0.001 0.901 0.002 21 N 0.001 0.002 0.010 0.001 0.001 0.001 0.001 0.001 0.018 0.004 0.001 0.001 0.026 0.001 0.002 0.932 22 V 0.862 0.009 0.081 0.017 0.001 0.001 0.001 0.001 0.001 0.001 0.003 0.005 0.016 0.001 0.001 0.006 23 S 0.001 0.001 0.002 0.001 0.001 0.986 0.001 0.001 0.001 0.001 0.001 0.003 0.008 0.001 0.001 0.001 24 L 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.992 0.001 0.006 0.001 0.001 0.001 25 R 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.994 0.005 0.001 0.001 0.001 26 E 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.998 0.001 0.001 0.001 27 F 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.002 0.995 0.001 0.001 0.001 28 A 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.995 0.001 0.001 0.001 29 R 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.003 0.990 0.002 0.001 0.001 30 A 0.001 0.001 0.001 0.001 0.001 0.001 0.005 0.001 0.001 0.001 0.001 0.001 0.032 0.955 0.001 0.007 31 M 0.001 0.001 0.006 0.001 0.001 0.001 0.007 0.002 0.001 0.001 0.001 0.001 0.066 0.001 0.916 0.002 32 E 0.001 0.002 0.005 0.001 0.001 0.001 0.002 0.001 0.003 0.001 0.001 0.001 0.033 0.001 0.001 0.951 33 I 0.880 0.016 0.051 0.019 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.002 0.014 0.001 0.003 0.013 34 A 0.002 0.001 0.072 0.002 0.001 0.890 0.002 0.001 0.001 0.001 0.001 0.003 0.025 0.001 0.001 0.001 35 P 0.001 0.006 0.001 0.001 0.001 0.017 0.001 0.001 0.001 0.001 0.965 0.001 0.009 0.001 0.001 0.001 36 S 0.001 0.030 0.001 0.004 0.001 0.001 0.001 0.001 0.001 0.001 0.003 0.958 0.003 0.001 0.001 0.001 37 T 0.001 0.001 0.016 0.005 0.001 0.040 0.003 0.001 0.001 0.001 0.007 0.030 0.889 0.001 0.001 0.005 38 A 0.001 0.002 0.010 0.002 0.001 0.026 0.002 0.001 0.001 0.001 0.064 0.017 0.875 0.001 0.001 0.001 39 S 0.001 0.016 0.002 0.011 0.001 0.003 0.001 0.001 0.001 0.001 0.013 0.193 0.755 0.001 0.001 0.001 40 R 0.001 0.001 0.001 0.007 0.001 0.001 0.001 0.001 0.001 0.001 0.002 0.004 0.974 0.002 0.002 0.004 41 L 0.001 0.002 0.029 0.003 0.001 0.003 0.011 0.001 0.001 0.001 0.002 0.003 0.904 0.010 0.003 0.027 42 L 0.001 0.001 0.003 0.001 0.017 0.001 0.160 0.001 0.001 0.001 0.001 0.001 0.055 0.755 0.002 0.003 43 T 0.001 0.002 0.006 0.002 0.001 0.001 0.003 0.076 0.001 0.001 0.001 0.001 0.041 0.002 0.857 0.006 44 G 0.003 0.005 0.006 0.004 0.001 0.003 0.003 0.001 0.094 0.056 0.015 0.002 0.062 0.004 0.003 0.740 45 K 0.891 0.018 0.023 0.006 0.001 0.002 0.007 0.001 0.001 0.001 0.003 0.020 0.017 0.002 0.003 0.006 46 A 0.020 0.039 0.726 0.063 0.001 0.032 0.010 0.004 0.001 0.001 0.011 0.018 0.041 0.002 0.013 0.018 47 A 0.025 0.112 0.325 0.257 0.010 0.127 0.013 0.002 0.007 0.003 0.011 0.011 0.046 0.001 0.002 0.047 48 L 0.024 0.177 0.116 0.593 0.001 0.023 0.001 0.003 0.001 0.001 0.019 0.016 0.020 0.001 0.001 0.004 49 T 0.001 0.003 0.006 0.011 0.001 0.922 0.001 0.001 0.001 0.003 0.005 0.023 0.023 0.001 0.001 0.001 50 P 0.001 0.001 0.001 0.001 0.001 0.025 0.001 0.001 0.001 0.001 0.952 0.004 0.018 0.001 0.001 0.001 51 E 0.001 0.008 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.003 0.977 0.011 0.001 0.001 0.001 52 M 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.002 0.010 0.984 0.001 0.001 0.001 53 A 0.001 0.001 0.006 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.004 0.985 0.001 0.001 0.001 54 I 0.001 0.002 0.001 0.006 0.001 0.002 0.001 0.001 0.001 0.001 0.001 0.008 0.978 0.001 0.001 0.001 55 K 0.001 0.001 0.001 0.008 0.001 0.014 0.001 0.001 0.001 0.001 0.003 0.003 0.963 0.003 0.001 0.003 56 L 0.001 0.001 0.001 0.001 0.001 0.006 0.001 0.001 0.001 0.001 0.009 0.003 0.977 0.001 0.001 0.001 57 S 0.001 0.005 0.001 0.003 0.001 0.001 0.001 0.001 0.001 0.001 0.003 0.018 0.963 0.001 0.001 0.003 58 V 0.001 0.001 0.001 0.002 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.003 0.984 0.001 0.001 0.003 59 V 0.001 0.001 0.017 0.002 0.007 0.001 0.087 0.001 0.001 0.001 0.001 0.001 0.253 0.586 0.004 0.038 60 I 0.002 0.006 0.030 0.009 0.001 0.003 0.013 0.039 0.001 0.001 0.003 0.003 0.210 0.006 0.663 0.013 61 G 0.007 0.010 0.024 0.010 0.002 0.018 0.015 0.002 0.039 0.044 0.006 0.004 0.232 0.012 0.004 0.571 62 S 0.579 0.033 0.031 0.032 0.001 0.009 0.003 0.008 0.001 0.002 0.062 0.034 0.182 0.002 0.010 0.013 63 S 0.004 0.015 0.037 0.006 0.001 0.300 0.002 0.001 0.002 0.005 0.044 0.169 0.406 0.001 0.001 0.005 64 P 0.001 0.002 0.002 0.003 0.001 0.032 0.001 0.001 0.001 0.001 0.540 0.063 0.355 0.001 0.001 0.001 65 Q 0.001 0.016 0.002 0.006 0.001 0.001 0.001 0.001 0.001 0.001 0.009 0.753 0.209 0.001 0.001 0.001 66 M 0.001 0.001 0.001 0.002 0.001 0.002 0.001 0.001 0.001 0.001 0.002 0.005 0.986 0.001 0.001 0.001 67 W 0.001 0.002 0.004 0.001 0.001 0.003 0.005 0.001 0.001 0.001 0.002 0.008 0.973 0.001 0.001 0.001 68 L 0.001 0.001 0.001 0.003 0.001 0.005 0.001 0.001 0.001 0.001 0.002 0.011 0.972 0.001 0.002 0.001 69 N 0.001 0.001 0.002 0.004 0.001 0.004 0.001 0.001 0.001 0.001 0.004 0.007 0.964 0.001 0.001 0.010 70 L 0.001 0.001 0.001 0.002 0.001 0.002 0.001 0.001 0.001 0.001 0.007 0.009 0.971 0.002 0.002 0.003 71 Q 0.001 0.002 0.008 0.002 0.001 0.002 0.004 0.001 0.001 0.001 0.006 0.014 0.945 0.009 0.004 0.005 72 N 0.001 0.001 0.002 0.001 0.001 0.003 0.002 0.001 0.001 0.001 0.003 0.010 0.963 0.001 0.006 0.005 73 A 0.002 0.007 0.011 0.004 0.001 0.003 0.010 0.001 0.001 0.001 0.011 0.007 0.879 0.010 0.004 0.051 74 W 0.009 0.010 0.058 0.022 0.001 0.005 0.004 0.002 0.001 0.001 0.006 0.034 0.806 0.001 0.028 0.014 75 S 0.001 0.001 0.006 0.002 0.001 0.163 0.002 0.001 0.001 0.001 0.007 0.011 0.796 0.001 0.001 0.007 76 L 0.001 0.004 0.001 0.001 0.001 0.010 0.001 0.001 0.001 0.001 0.354 0.017 0.609 0.001 0.001 0.001 77 A 0.001 0.006 0.002 0.002 0.001 0.002 0.001 0.001 0.001 0.001 0.008 0.475 0.497 0.001 0.003 0.001 78 E 0.001 0.001 0.002 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.002 0.004 0.975 0.002 0.002 0.008 79 A 0.001 0.001 0.010 0.002 0.001 0.003 0.005 0.001 0.001 0.001 0.004 0.006 0.960 0.003 0.002 0.004 80 E 0.001 0.003 0.011 0.004 0.001 0.004 0.010 0.001 0.001 0.001 0.006 0.007 0.926 0.008 0.007 0.012 81 K 0.004 0.007 0.021 0.018 0.001 0.006 0.008 0.002 0.001 0.001 0.009 0.012 0.845 0.010 0.017 0.040 82 T 0.011 0.013 0.059 0.015 0.004 0.023 0.050 0.001 0.002 0.001 0.013 0.010 0.605 0.080 0.012 0.102 83 V 0.016 0.092 0.201 0.048 0.001 0.016 0.017 0.013 0.001 0.001 0.031 0.021 0.420 0.005 0.086 0.032 84 D 0.012 0.035 0.086 0.041 0.002 0.219 0.010 0.003 0.008 0.008 0.017 0.049 0.428 0.004 0.007 0.070 85 V 0.041 0.041 0.053 0.039 0.001 0.041 0.007 0.003 0.001 0.001 0.363 0.027 0.365 0.003 0.004 0.010 86 S 0.007 0.102 0.069 0.061 0.002 0.070 0.008 0.004 0.003 0.001 0.034 0.368 0.247 0.006 0.008 0.010 87 R 0.008 0.029 0.095 0.082 0.005 0.055 0.022 0.005 0.002 0.001 0.058 0.036 0.547 0.014 0.014 0.027 88 L 0.009 0.081 0.171 0.123 0.004 0.042 0.020 0.010 0.003 0.001 0.033 0.061 0.391 0.007 0.020 0.024 89 R 0.019 0.037 0.135 0.188 0.003 0.050 0.013 0.012 0.006 0.003 0.042 0.025 0.393 0.008 0.016 0.050 90 R 0.034 0.075 0.232 0.318 0.002 0.026 0.009 0.005 0.006 0.002 0.023 0.023 0.186 0.004 0.009 0.045 91 L 0.025 0.035 0.238 0.470 0.005 0.046 0.007 0.003 0.002 0.001 0.011 0.011 0.114 0.003 0.004 0.023 92 V 0.016 0.054 0.197 0.448 0.014 0.128 0.013 0.004 0.001 0.002 0.015 0.010 0.080 0.004 0.002 0.011 93 T 0.009 0.085 0.061 0.399 0.023 0.233 0.012 0.016 0.003 0.003 0.053 0.022 0.065 0.006 0.004 0.006 94 Q 0.008 0.196 0.070 0.373 0.015 0.068 0.010 0.024 0.013 0.004 0.093 0.033 0.062 0.005 0.008 0.018 95 S 0.028 0.133 0.164 0.456 0.009 0.025 0.011 0.008 0.018 0.005 0.013 0.041 0.046 0.004 0.007 0.032 96 T 0.030 0.019 0.198 0.165 0.131 0.224 0.086 0.005 0.004 0.009 0.021 0.018 0.063 0.013 0.004 0.012 97 P 0.012 0.132 0.078 0.137 0.056 0.112 0.021 0.140 0.003 0.004 0.198 0.022 0.046 0.013 0.018 0.007