# This file is the result of combining several RDB files, specifically # T0387.t04.str2.rdb (weight 1.54425) # T0387.t04.str4.rdb (weight 0.924988) # T0387.t04.pb.rdb (weight 0.789901) # T0387.t04.bys.rdb (weight 0.748322) # T0387.t04.alpha.rdb (weight 0.678173) # These files were combined by translating their predictions into EHL # predictions with tables generated by compare-real, and then combining # those predictions with weights proportional to their mutual information # with the EHL alphabet. The comments from the individual files follow. # # Comments from T0387.t04.str2.rdb # ============================================ # TARGET T0387 # Using neural net dunbrack-40pc-3157-t04-IDGaaH13-3-13-7-13-9-13-11-str2-seeded.net # This is a 4-layer network, with # window units # 3 13 # 7 13 # 9 13 # 11 13 (1 str2 ) # The input amino acid frequencies were determined from # alignment T0387.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 946.995 # # ============================================ # Comments from T0387.t04.str4.rdb # ============================================ # TARGET T0387 # Using neural net dunbrack-40pc-3157-t04-IDGaaH13-3-13-7-13-9-13-11-str4-seeded.net # This is a 4-layer network, with # window units # 3 13 # 7 13 # 9 13 # 11 21 (1 str4 ) # The input amino acid frequencies were determined from # alignment T0387.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 946.995 # # ============================================ # Comments from T0387.t04.pb.rdb # ============================================ # TARGET T0387 # Using neural net dunbrack-40pc-3157-t04-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 T0387.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 946.995 # # ============================================ # Comments from T0387.t04.bys.rdb # ============================================ # TARGET T0387 # Using neural net dunbrack-40pc-3157-t04-IDGaaH13-3-13-7-13-9-13-11-bys-seeded.net # This is a 4-layer network, with # window units # 3 13 # 7 13 # 9 13 # 11 11 (1 Bystroff ) # The input amino acid frequencies were determined from # alignment T0387.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 946.995 # # ============================================ # Comments from T0387.t04.alpha.rdb # ============================================ # TARGET T0387 # Using neural net dunbrack-40pc-3157-t04-IDGaaH13-3-13-7-13-9-13-11-alpha-seeded.net # This is a 4-layer network, with # window units # 3 13 # 7 13 # 9 13 # 11 11 (1 ABCDEFGHIST ) # The input amino acid frequencies were determined from # alignment T0387.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 946.995 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 S 0.2385 0.0846 0.6769 2 M 0.2924 0.0590 0.6486 3 K 0.4077 0.0210 0.5713 4 P 0.5454 0.0177 0.4370 5 K 0.6808 0.0188 0.3004 6 L 0.7654 0.0055 0.2290 7 C 0.7855 0.0073 0.2072 8 R 0.8004 0.0053 0.1943 9 L 0.7751 0.0072 0.2177 10 A 0.6988 0.0166 0.2846 11 K 0.5486 0.0472 0.4042 12 G 0.3100 0.0458 0.6442 13 E 0.1860 0.1875 0.6266 14 N 0.1607 0.1270 0.7123 15 G 0.2197 0.0712 0.7091 16 Y 0.3968 0.0579 0.5453 17 G 0.6318 0.0232 0.3450 18 F 0.7702 0.0092 0.2206 19 H 0.7784 0.0074 0.2142 20 L 0.7597 0.0102 0.2300 21 N 0.6620 0.0405 0.2975 22 A 0.5397 0.0519 0.4083 23 I 0.4388 0.1117 0.4494 24 R 0.2661 0.1376 0.5964 25 G 0.1697 0.0973 0.7330 26 L 0.2094 0.0701 0.7205 27 P 0.1931 0.1211 0.6859 28 G 0.2636 0.0754 0.6610 29 S 0.5742 0.0340 0.3918 30 F 0.7062 0.0233 0.2705 31 I 0.6932 0.0385 0.2684 32 K 0.6488 0.0800 0.2712 33 E 0.7075 0.0389 0.2536 34 V 0.5517 0.0795 0.3688 35 Q 0.3687 0.0782 0.5531 36 K 0.1434 0.1825 0.6741 37 G 0.0919 0.1094 0.7987 38 G 0.1570 0.0645 0.7785 39 P 0.0972 0.3976 0.5053 40 A 0.0863 0.6207 0.2930 41 D 0.0694 0.6548 0.2758 42 L 0.0726 0.5386 0.3888 43 A 0.0831 0.2531 0.6638 44 G 0.0836 0.0924 0.8241 45 L 0.1829 0.0436 0.7736 46 E 0.1973 0.0336 0.7691 47 D 0.0905 0.3162 0.5934 48 E 0.0545 0.2248 0.7207 49 D 0.3184 0.1068 0.5748 50 V 0.5969 0.0923 0.3108 51 I 0.7228 0.0564 0.2208 52 I 0.7877 0.0230 0.1893 53 E 0.7792 0.0161 0.2047 54 V 0.6981 0.0450 0.2569 55 N 0.3880 0.0469 0.5650 56 G 0.2188 0.0542 0.7271 57 V 0.5043 0.0313 0.4644 58 N 0.5320 0.0286 0.4393 59 V 0.3701 0.1660 0.4638 60 L 0.2007 0.1811 0.6182 61 D 0.1336 0.1038 0.7627 62 E 0.2071 0.0706 0.7223 63 P 0.1777 0.1000 0.7224 64 Y 0.0243 0.6981 0.2776 65 E 0.0099 0.8556 0.1345 66 K 0.0086 0.9162 0.0752 67 V 0.0083 0.9220 0.0697 68 V 0.0083 0.9221 0.0696 69 D 0.0083 0.9232 0.0686 70 R 0.0083 0.9214 0.0702 71 I 0.0090 0.9090 0.0820 72 Q 0.0109 0.8559 0.1331 73 S 0.0204 0.6805 0.2991 74 S 0.0727 0.2057 0.7216 75 G 0.0725 0.0877 0.8398 76 K 0.1993 0.0692 0.7315 77 N 0.4752 0.0296 0.4952 78 V 0.7036 0.0106 0.2858 79 T 0.7844 0.0066 0.2090 80 L 0.8156 0.0045 0.1799 81 L 0.8090 0.0056 0.1853 82 V 0.7727 0.0067 0.2206 83 C 0.6554 0.0258 0.3188 84 G 0.4339 0.0354 0.5308 85 K 0.2969 0.0929 0.6102 86 K 0.2732 0.0726 0.6542 87 A 0.2234 0.1086 0.6680 88 Q 0.1988 0.1959 0.6053 89 D 0.2027 0.2120 0.5853 90 T 0.2084 0.2052 0.5864 91 V 0.2214 0.1640 0.6146 92 S 0.2385 0.0846 0.6769 93 M 0.2924 0.0590 0.6486 94 K 0.4077 0.0210 0.5713 95 P 0.5454 0.0177 0.4370 96 K 0.6808 0.0188 0.3004 97 L 0.7654 0.0055 0.2290 98 C 0.7855 0.0073 0.2072 99 R 0.8004 0.0053 0.1943 100 L 0.7751 0.0072 0.2177 101 A 0.6988 0.0166 0.2846 102 K 0.5486 0.0472 0.4042 103 G 0.3100 0.0458 0.6442 104 E 0.1860 0.1875 0.6266 105 N 0.1607 0.1270 0.7123 106 G 0.2197 0.0712 0.7091 107 Y 0.3968 0.0579 0.5453 108 G 0.6318 0.0232 0.3450 109 F 0.7702 0.0092 0.2206 110 H 0.7784 0.0074 0.2142 111 L 0.7597 0.0102 0.2300 112 N 0.6620 0.0405 0.2975 113 A 0.5397 0.0519 0.4083 114 I 0.4388 0.1117 0.4494 115 R 0.2661 0.1376 0.5964 116 G 0.1697 0.0973 0.7330 117 L 0.2094 0.0701 0.7205 118 P 0.1931 0.1211 0.6859 119 G 0.2636 0.0754 0.6610 120 S 0.5742 0.0340 0.3918 121 F 0.7062 0.0233 0.2705 122 I 0.6932 0.0385 0.2684 123 K 0.6488 0.0800 0.2712 124 E 0.7075 0.0389 0.2536 125 V 0.5517 0.0795 0.3688 126 Q 0.3687 0.0782 0.5531 127 K 0.1434 0.1825 0.6741 128 G 0.0919 0.1094 0.7987 129 G 0.1570 0.0645 0.7785 130 P 0.0972 0.3976 0.5053 131 A 0.0863 0.6207 0.2930 132 D 0.0694 0.6548 0.2758 133 L 0.0726 0.5386 0.3888 134 A 0.0831 0.2531 0.6638 135 G 0.0836 0.0924 0.8241 136 L 0.1829 0.0436 0.7736 137 E 0.1973 0.0336 0.7691 138 D 0.0905 0.3162 0.5934 139 E 0.0545 0.2248 0.7207 140 D 0.3184 0.1068 0.5748 141 V 0.5969 0.0923 0.3108 142 I 0.7228 0.0564 0.2208 143 I 0.7877 0.0230 0.1893 144 E 0.7792 0.0161 0.2047 145 V 0.6981 0.0450 0.2569 146 N 0.3880 0.0469 0.5650 147 G 0.2188 0.0542 0.7271 148 V 0.5043 0.0313 0.4644 149 N 0.5320 0.0286 0.4393 150 V 0.3701 0.1660 0.4638 151 L 0.2007 0.1811 0.6182 152 D 0.1336 0.1038 0.7627 153 E 0.2071 0.0706 0.7223 154 P 0.1777 0.1000 0.7224 155 Y 0.0243 0.6981 0.2776 156 E 0.0099 0.8556 0.1345 157 K 0.0086 0.9162 0.0752 158 V 0.0083 0.9220 0.0697 159 V 0.0083 0.9221 0.0696 160 D 0.0083 0.9232 0.0686 161 R 0.0083 0.9214 0.0702 162 I 0.0090 0.9090 0.0820 163 Q 0.0109 0.8559 0.1331 164 S 0.0204 0.6805 0.2991 165 S 0.0727 0.2057 0.7216 166 G 0.0725 0.0877 0.8398 167 K 0.1993 0.0692 0.7315 168 N 0.4752 0.0296 0.4952 169 V 0.7036 0.0106 0.2858 170 T 0.7844 0.0066 0.2090 171 L 0.8156 0.0045 0.1799 172 L 0.8090 0.0056 0.1853 173 V 0.7727 0.0067 0.2206 174 C 0.6554 0.0258 0.3188 175 G 0.4339 0.0354 0.5308 176 K 0.2969 0.0929 0.6102 177 K 0.2732 0.0726 0.6542 178 A 0.2234 0.1086 0.6680 179 Q 0.1988 0.1959 0.6053 180 D 0.2027 0.2120 0.5853 181 T 0.2084 0.2052 0.5864 182 V 0.2214 0.1640 0.6146