# This file is the result of combining several RDB files, specifically # T0423.t06.str2.rdb (weight 1.54425) # T0423.t06.str4.rdb (weight 0.924988) # T0423.t06.pb.rdb (weight 0.789901) # T0423.t06.bys.rdb (weight 0.748322) # T0423.t06.alpha.rdb (weight 0.678173) # T0423.t04.str2.rdb (weight 1.54425) # T0423.t04.str4.rdb (weight 0.924988) # T0423.t04.pb.rdb (weight 0.789901) # T0423.t04.bys.rdb (weight 0.748322) # T0423.t04.alpha.rdb (weight 0.678173) # T0423.t2k.str2.rdb (weight 1.54425) # T0423.t2k.str4.rdb (weight 0.924988) # T0423.t2k.pb.rdb (weight 0.789901) # T0423.t2k.bys.rdb (weight 0.748322) # T0423.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 T0423.t06.str2.rdb # ============================================ # TARGET T0423 # 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 T0423.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 910.806 # # ============================================ # Comments from T0423.t06.str4.rdb # ============================================ # TARGET T0423 # 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 T0423.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 910.806 # # ============================================ # Comments from T0423.t06.pb.rdb # ============================================ # TARGET T0423 # 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 T0423.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 910.806 # # ============================================ # Comments from T0423.t06.bys.rdb # ============================================ # TARGET T0423 # 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 T0423.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 910.806 # # ============================================ # Comments from T0423.t06.alpha.rdb # ============================================ # TARGET T0423 # 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 T0423.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 910.806 # # ============================================ # Comments from T0423.t04.str2.rdb # ============================================ # TARGET T0423 # 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 T0423.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 1672.69 # # ============================================ # Comments from T0423.t04.str4.rdb # ============================================ # TARGET T0423 # 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 T0423.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 1672.69 # # ============================================ # Comments from T0423.t04.pb.rdb # ============================================ # TARGET T0423 # 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 T0423.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 1672.69 # # ============================================ # Comments from T0423.t04.bys.rdb # ============================================ # TARGET T0423 # 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 T0423.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 1672.69 # # ============================================ # Comments from T0423.t04.alpha.rdb # ============================================ # TARGET T0423 # 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 T0423.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 1672.69 # # ============================================ # Comments from T0423.t2k.str2.rdb # ============================================ # TARGET T0423 # 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 T0423.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 52.0829 # # ============================================ # Comments from T0423.t2k.str4.rdb # ============================================ # TARGET T0423 # 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 T0423.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 52.0829 # # ============================================ # Comments from T0423.t2k.pb.rdb # ============================================ # TARGET T0423 # 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 T0423.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 52.0829 # # ============================================ # Comments from T0423.t2k.bys.rdb # ============================================ # TARGET T0423 # 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 T0423.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 52.0829 # # ============================================ # Comments from T0423.t2k.alpha.rdb # ============================================ # TARGET T0423 # 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 T0423.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 52.0829 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.1635 0.2402 0.5962 2 S 0.1126 0.3518 0.5356 3 D 0.0899 0.4906 0.4195 4 V 0.0772 0.6043 0.3185 5 I 0.0284 0.8162 0.1554 6 E 0.0145 0.8862 0.0994 7 G 0.0111 0.9042 0.0847 8 R 0.0131 0.9012 0.0856 9 L 0.0123 0.8955 0.0923 10 K 0.0102 0.8865 0.1033 11 E 0.0284 0.7738 0.1978 12 L 0.0744 0.3552 0.5704 13 G 0.0860 0.1082 0.8058 14 F 0.2962 0.0827 0.6210 15 T 0.4271 0.0746 0.4983 16 L 0.3310 0.0384 0.6306 17 P 0.1891 0.1784 0.6325 18 V 0.1870 0.1942 0.6187 19 A 0.2028 0.1819 0.6153 20 A 0.1867 0.1962 0.6171 21 A 0.2194 0.1129 0.6678 22 P 0.1472 0.2377 0.6151 23 A 0.1653 0.1983 0.6363 24 A 0.2189 0.1488 0.6323 25 N 0.2296 0.1756 0.5949 26 Y 0.3318 0.1334 0.5348 27 V 0.3968 0.0831 0.5201 28 P 0.4463 0.1557 0.3980 29 F 0.5927 0.1157 0.2916 30 T 0.6251 0.0965 0.2784 31 I 0.5627 0.0974 0.3399 32 S 0.3510 0.1058 0.5432 33 G 0.2016 0.0900 0.7084 34 N 0.3149 0.0701 0.6150 35 L 0.6647 0.0240 0.3113 36 L 0.7622 0.0122 0.2256 37 Y 0.7842 0.0091 0.2067 38 V 0.7383 0.0219 0.2398 39 S 0.6024 0.0423 0.3552 40 G 0.4134 0.0685 0.5182 41 Q 0.4242 0.0510 0.5249 42 L 0.4186 0.0265 0.5549 43 P 0.3765 0.0336 0.5899 44 M 0.2959 0.1033 0.6008 45 E 0.2507 0.0765 0.6728 46 S 0.1540 0.1657 0.6803 47 G 0.0919 0.1224 0.7857 48 K 0.3200 0.0728 0.6073 49 I 0.5744 0.0310 0.3946 50 A 0.6835 0.0264 0.2901 51 V 0.6895 0.0317 0.2789 52 T 0.6254 0.0504 0.3241 53 G 0.4955 0.0682 0.4364 54 L 0.4393 0.1091 0.4516 55 V 0.3081 0.1179 0.5740 56 G 0.2026 0.0994 0.6980 57 R 0.1741 0.2185 0.6074 58 D 0.2275 0.1452 0.6273 59 V 0.3062 0.0862 0.6076 60 D 0.1931 0.0402 0.7667 61 V 0.0199 0.7203 0.2598 62 A 0.0109 0.8452 0.1439 63 S 0.0124 0.8712 0.1163 64 A 0.0116 0.8964 0.0920 65 Q 0.0094 0.9085 0.0821 66 R 0.0085 0.9149 0.0766 67 A 0.0087 0.9161 0.0752 68 A 0.0093 0.9168 0.0739 69 E 0.0083 0.9235 0.0682 70 L 0.0083 0.9228 0.0689 71 C 0.0083 0.9244 0.0673 72 A 0.0083 0.9222 0.0695 73 V 0.0083 0.9239 0.0679 74 N 0.0083 0.9250 0.0668 75 I 0.0083 0.9229 0.0688 76 L 0.0083 0.9234 0.0683 77 A 0.0083 0.9225 0.0692 78 Q 0.0083 0.9242 0.0676 79 V 0.0085 0.9119 0.0796 80 K 0.0083 0.9215 0.0702 81 A 0.0083 0.9223 0.0693 82 A 0.0092 0.9087 0.0821 83 L 0.0170 0.8495 0.1336 84 N 0.0231 0.7287 0.2482 85 G 0.0362 0.5817 0.3821 86 D 0.0541 0.4478 0.4982 87 L 0.0384 0.5919 0.3697 88 S 0.0444 0.6459 0.3098 89 K 0.0692 0.6206 0.3101 90 I 0.0687 0.6954 0.2359 91 R 0.0850 0.6693 0.2457 92 R 0.1654 0.5554 0.2792 93 V 0.3533 0.3890 0.2577 94 I 0.5079 0.2335 0.2586 95 K 0.6066 0.1242 0.2692 96 L 0.6026 0.1205 0.2769 97 N 0.6196 0.0935 0.2869 98 G 0.6809 0.0565 0.2626 99 F 0.6933 0.0602 0.2465 100 V 0.5791 0.1162 0.3047 101 A 0.3690 0.1801 0.4510 102 S 0.2135 0.1546 0.6319 103 V 0.1418 0.2034 0.6548 104 P 0.0504 0.4912 0.4584 105 E 0.0421 0.5251 0.4328 106 F 0.0560 0.6286 0.3154 107 V 0.0547 0.6959 0.2495 108 E 0.0566 0.6896 0.2538 109 Q 0.0683 0.7146 0.2170 110 H 0.0523 0.7767 0.1710 111 L 0.0476 0.8131 0.1393 112 V 0.0467 0.8164 0.1369 113 I 0.0578 0.7403 0.2020 114 N 0.0483 0.5852 0.3665 115 G 0.0438 0.4306 0.5256 116 A 0.0470 0.6447 0.3082 117 S 0.0228 0.8013 0.1759 118 N 0.0145 0.8709 0.1147 119 L 0.0170 0.8843 0.0986 120 I 0.0228 0.8836 0.0935 121 A 0.0249 0.8750 0.1000 122 T 0.0414 0.8284 0.1302 123 V 0.0816 0.6666 0.2518 124 L 0.1121 0.3787 0.5092 125 G 0.0852 0.1471 0.7678 126 E 0.1559 0.1039 0.7402 127 P 0.1052 0.1992 0.6957 128 G 0.0717 0.1402 0.7880 129 R 0.1769 0.0883 0.7348 130 H 0.2552 0.1500 0.5948 131 A 0.2525 0.3262 0.4214 132 R 0.2866 0.3800 0.3334 133 A 0.4078 0.3393 0.2529 134 A 0.4455 0.2951 0.2593 135 V 0.5235 0.2149 0.2616 136 G 0.4404 0.2186 0.3410 137 M 0.3292 0.3077 0.3631 138 A 0.2939 0.2558 0.4503 139 S 0.2917 0.1724 0.5359 140 L 0.2820 0.0767 0.6413 141 P 0.2109 0.1379 0.6511 142 F 0.1164 0.1889 0.6946 143 N 0.1014 0.1102 0.7883 144 A 0.2743 0.0512 0.6745 145 S 0.5313 0.0271 0.4416 146 V 0.6927 0.0124 0.2949 147 E 0.7856 0.0068 0.2076 148 I 0.8037 0.0064 0.1899 149 D 0.7811 0.0101 0.2088 150 A 0.8084 0.0065 0.1851 151 I 0.8160 0.0051 0.1789 152 V 0.7891 0.0087 0.2022 153 E 0.7779 0.0079 0.2142 154 I 0.7162 0.0210 0.2628 155 D 0.4860 0.0344 0.4796 156 V 0.2918 0.1196 0.5887