# This file is the result of combining several RDB files, specifically # T0407.t06.str2.rdb (weight 1.54425) # T0407.t06.str4.rdb (weight 0.924988) # T0407.t06.pb.rdb (weight 0.789901) # T0407.t06.bys.rdb (weight 0.748322) # T0407.t06.alpha.rdb (weight 0.678173) # T0407.t04.str2.rdb (weight 1.54425) # T0407.t04.str4.rdb (weight 0.924988) # T0407.t04.pb.rdb (weight 0.789901) # T0407.t04.bys.rdb (weight 0.748322) # T0407.t04.alpha.rdb (weight 0.678173) # T0407.t2k.str2.rdb (weight 1.54425) # T0407.t2k.str4.rdb (weight 0.924988) # T0407.t2k.pb.rdb (weight 0.789901) # T0407.t2k.bys.rdb (weight 0.748322) # T0407.t2k.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 T0407.t06.str2.rdb # ============================================ # TARGET T0407 # Using neural net dunbrack-40pc-3157-t06-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 T0407.t06-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 2 # # ============================================ # Comments from T0407.t06.str4.rdb # ============================================ # TARGET T0407 # Using neural net dunbrack-40pc-3157-t06-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 T0407.t06-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 2 # # ============================================ # Comments from T0407.t06.pb.rdb # ============================================ # TARGET T0407 # 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 T0407.t06-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 2 # # ============================================ # Comments from T0407.t06.bys.rdb # ============================================ # TARGET T0407 # Using neural net dunbrack-40pc-3157-t06-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 T0407.t06-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 2 # # ============================================ # Comments from T0407.t06.alpha.rdb # ============================================ # TARGET T0407 # Using neural net dunbrack-40pc-3157-t06-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 T0407.t06-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 2 # # ============================================ # Comments from T0407.t04.str2.rdb # ============================================ # TARGET T0407 # 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 T0407.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 2 # # ============================================ # Comments from T0407.t04.str4.rdb # ============================================ # TARGET T0407 # 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 T0407.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 2 # # ============================================ # Comments from T0407.t04.pb.rdb # ============================================ # TARGET T0407 # 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 T0407.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 2 # # ============================================ # Comments from T0407.t04.bys.rdb # ============================================ # TARGET T0407 # 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 T0407.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 2 # # ============================================ # Comments from T0407.t04.alpha.rdb # ============================================ # TARGET T0407 # 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 T0407.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 2 # # ============================================ # Comments from T0407.t2k.str2.rdb # ============================================ # TARGET T0407 # Using neural net dunbrack-40pc-3157-t2k-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 T0407.t2k-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 8 # # ============================================ # Comments from T0407.t2k.str4.rdb # ============================================ # TARGET T0407 # Using neural net dunbrack-40pc-3157-t2k-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 T0407.t2k-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 8 # # ============================================ # Comments from T0407.t2k.pb.rdb # ============================================ # TARGET T0407 # Using neural net dunbrack-40pc-3157-t2k-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 T0407.t2k-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 8 # # ============================================ # Comments from T0407.t2k.bys.rdb # ============================================ # TARGET T0407 # Using neural net dunbrack-40pc-3157-t2k-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 T0407.t2k-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 8 # # ============================================ # Comments from T0407.t2k.alpha.rdb # ============================================ # TARGET T0407 # Using neural net dunbrack-40pc-3157-t2k-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 T0407.t2k-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 8 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 R 0.2081 0.1708 0.6211 2 S 0.1608 0.1034 0.7358 3 L 0.0141 0.7602 0.2257 4 Q 0.0093 0.8685 0.1222 5 G 0.0085 0.9147 0.0768 6 I 0.0085 0.9122 0.0793 7 R 0.0084 0.9176 0.0740 8 E 0.0083 0.9112 0.0805 9 A 0.0088 0.9030 0.0882 10 L 0.0107 0.8504 0.1389 11 D 0.0197 0.7035 0.2768 12 N 0.0330 0.4012 0.5658 13 R 0.0767 0.2443 0.6791 14 R 0.2430 0.1808 0.5761 15 T 0.4398 0.1547 0.4055 16 A 0.5667 0.1704 0.2629 17 A 0.6248 0.1588 0.2164 18 Y 0.5477 0.2128 0.2396 19 F 0.4125 0.2874 0.3002 20 H 0.2269 0.4482 0.3250 21 E 0.1351 0.5383 0.3266 22 L 0.1320 0.5469 0.3210 23 L 0.1890 0.4301 0.3810 24 I 0.1858 0.3170 0.4972 25 G 0.1548 0.2026 0.6426 26 R 0.0844 0.4191 0.4965 27 E 0.0176 0.7720 0.2104 28 D 0.0122 0.8309 0.1569 29 L 0.0137 0.8128 0.1735 30 L 0.0179 0.7899 0.1922 31 R 0.0172 0.7893 0.1935 32 P 0.0089 0.8881 0.1030 33 F 0.0104 0.8608 0.1289 34 F 0.0153 0.8668 0.1179 35 E 0.0155 0.8433 0.1412 36 K 0.0350 0.7169 0.2480 37 C 0.1586 0.4455 0.3959 38 V 0.4109 0.1885 0.4006 39 K 0.5755 0.0839 0.3406 40 I 0.5952 0.0804 0.3244 41 E 0.5364 0.0923 0.3713 42 E 0.5277 0.1029 0.3694 43 V 0.4072 0.1221 0.4708 44 S 0.3310 0.1075 0.5615 45 R 0.3584 0.1199 0.5217 46 N 0.2898 0.0803 0.6299 47 E 0.2216 0.2663 0.5121 48 Q 0.1526 0.1604 0.6870 49 G 0.2092 0.0748 0.7160 50 V 0.4193 0.0243 0.5563 51 T 0.7106 0.0122 0.2773 52 L 0.7743 0.0093 0.2164 53 S 0.7854 0.0068 0.2077 54 I 0.7829 0.0070 0.2101 55 T 0.7617 0.0133 0.2250 56 N 0.6637 0.0219 0.3144 57 V 0.4344 0.0946 0.4710 58 T 0.2771 0.0857 0.6373 59 D 0.1812 0.2419 0.5769 60 L 0.1966 0.3387 0.4647 61 V 0.2721 0.3515 0.3764 62 L 0.3130 0.3810 0.3060 63 K 0.2937 0.4089 0.2974 64 L 0.3089 0.4078 0.2833 65 K 0.2858 0.3810 0.3333 66 K 0.2443 0.3189 0.4367 67 T 0.1906 0.2222 0.5872 68 A 0.1306 0.2249 0.6445 69 H 0.1375 0.1805 0.6821 70 D 0.1981 0.1059 0.6960 71 T 0.2311 0.1800 0.5889 72 L 0.3965 0.1559 0.4476 73 L 0.5426 0.0975 0.3599 74 V 0.6132 0.0562 0.3306 75 Y 0.5181 0.0516 0.4303 76 F 0.3617 0.1102 0.5282 77 R 0.2485 0.1775 0.5740 78 D 0.2138 0.1822 0.6040 79 M 0.2503 0.1752 0.5746 80 T 0.4212 0.0994 0.4794 81 L 0.5503 0.0617 0.3880 82 K 0.5372 0.0363 0.4265 83 P 0.4118 0.1166 0.4716 84 H 0.3158 0.1397 0.5445 85 T 0.3077 0.1318 0.5605 86 R 0.3017 0.1077 0.5906 87 Y 0.4822 0.0649 0.4529 88 T 0.6319 0.0275 0.3406 89 V 0.7441 0.0162 0.2397 90 R 0.7637 0.0108 0.2255 91 I 0.7568 0.0170 0.2262 92 G 0.6950 0.0219 0.2831 93 F 0.6195 0.0416 0.3389 94 K 0.4325 0.0878 0.4797 95 Q 0.3136 0.1260 0.5605 96 G 0.2399 0.1285 0.6316 97 I 0.3761 0.1054 0.5184 98 K 0.3064 0.0978 0.5958 99 G 0.1990 0.1006 0.7003 100 G 0.2002 0.1098 0.6901 101 D 0.3414 0.0686 0.5899 102 V 0.4952 0.0424 0.4624 103 N 0.5852 0.0406 0.3743 104 F 0.6841 0.0271 0.2887 105 E 0.7568 0.0204 0.2228 106 V 0.7400 0.0234 0.2366 107 T 0.6451 0.0778 0.2771 108 N 0.6927 0.0516 0.2558 109 F 0.6975 0.0441 0.2584 110 I 0.7197 0.0331 0.2471 111 V 0.6908 0.0390 0.2702 112 A 0.5446 0.0270 0.4285 113 P 0.3195 0.0980 0.5825 114 D 0.2362 0.1134 0.6504 115 K 0.1039 0.1924 0.7037 116 G 0.0603 0.1152 0.8245 117 L 0.2508 0.0526 0.6966 118 K 0.4154 0.0347 0.5499 119 Y 0.5751 0.0296 0.3953 120 T 0.7245 0.0161 0.2595 121 I 0.7373 0.0153 0.2474 122 S 0.6810 0.0184 0.3005 123 L 0.4696 0.0487 0.4817