# This file is the result of combining several RDB files, specifically # T0389.t04.str2.rdb (weight 1.54425) # T0389.t04.str4.rdb (weight 0.924988) # T0389.t04.pb.rdb (weight 0.789901) # T0389.t04.bys.rdb (weight 0.748322) # T0389.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 T0389.t04.str2.rdb # ============================================ # TARGET T0389 # 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 T0389.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 2356 # # ============================================ # Comments from T0389.t04.str4.rdb # ============================================ # TARGET T0389 # 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 T0389.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 2356 # # ============================================ # Comments from T0389.t04.pb.rdb # ============================================ # TARGET T0389 # 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 T0389.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 2356 # # ============================================ # Comments from T0389.t04.bys.rdb # ============================================ # TARGET T0389 # 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 T0389.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 2356 # # ============================================ # Comments from T0389.t04.alpha.rdb # ============================================ # TARGET T0389 # 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 T0389.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 2356 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.2778 0.0665 0.6557 2 I 0.2594 0.0737 0.6669 3 G 0.2644 0.1126 0.6230 4 T 0.3318 0.1434 0.5248 5 Q 0.4414 0.0671 0.4915 6 I 0.3645 0.0505 0.5850 7 V 0.1887 0.0232 0.7880 8 T 0.0152 0.7229 0.2619 9 E 0.0094 0.8665 0.1241 10 R 0.0088 0.9144 0.0769 11 L 0.0085 0.9188 0.0727 12 V 0.0084 0.9191 0.0726 13 A 0.0084 0.9179 0.0738 14 L 0.0088 0.9011 0.0901 15 L 0.0115 0.8547 0.1338 16 E 0.0162 0.6447 0.3391 17 S 0.0595 0.2509 0.6896 18 G 0.0617 0.0943 0.8440 19 T 0.1723 0.0770 0.7507 20 E 0.2186 0.1226 0.6588 21 K 0.3918 0.0624 0.5458 22 V 0.6962 0.0083 0.2955 23 L 0.7660 0.0076 0.2265 24 L 0.7913 0.0049 0.2038 25 I 0.7781 0.0113 0.2105 26 D 0.6614 0.0134 0.3252 27 S 0.4009 0.0537 0.5454 28 R 0.2980 0.0356 0.6664 29 P 0.1869 0.0642 0.7489 30 F 0.0777 0.4957 0.4266 31 V 0.0540 0.6737 0.2723 32 E 0.0573 0.7371 0.2056 33 Y 0.0833 0.6555 0.2612 34 N 0.0906 0.5661 0.3433 35 T 0.1038 0.4438 0.4524 36 S 0.1560 0.2667 0.5773 37 H 0.2588 0.1736 0.5676 38 I 0.2884 0.1269 0.5847 39 L 0.1967 0.2517 0.5516 40 E 0.2019 0.1825 0.6156 41 A 0.3521 0.1467 0.5012 42 I 0.5374 0.0953 0.3673 43 N 0.5238 0.0557 0.4206 44 I 0.4556 0.0588 0.4857 45 N 0.2835 0.0409 0.6757 46 C 0.0724 0.5703 0.3573 47 S 0.0230 0.7559 0.2210 48 K 0.0196 0.8314 0.1490 49 L 0.0238 0.8236 0.1526 50 M 0.0319 0.7955 0.1726 51 K 0.0401 0.7345 0.2254 52 R 0.0565 0.6609 0.2826 53 R 0.0831 0.5356 0.3812 54 L 0.1128 0.4440 0.4432 55 Q 0.1146 0.3788 0.5066 56 Q 0.1220 0.3498 0.5283 57 D 0.1017 0.3139 0.5845 58 K 0.1396 0.2961 0.5643 59 V 0.2529 0.2046 0.5425 60 L 0.2817 0.1460 0.5722 61 I 0.2393 0.1412 0.6194 62 T 0.1762 0.1349 0.6888 63 E 0.0145 0.7364 0.2491 64 L 0.0110 0.8454 0.1436 65 I 0.0128 0.8915 0.0956 66 Q 0.0112 0.8946 0.0942 67 H 0.0107 0.8962 0.0931 68 S 0.0107 0.8905 0.0988 69 A 0.0131 0.8581 0.1288 70 K 0.0194 0.8051 0.1755 71 H 0.0287 0.7246 0.2467 72 K 0.0616 0.5334 0.4049 73 V 0.1422 0.2225 0.6353 74 D 0.1541 0.1040 0.7419 75 I 0.2341 0.0913 0.6745 76 D 0.2058 0.0614 0.7329 77 C 0.1166 0.2408 0.6426 78 S 0.1327 0.1187 0.7486 79 Q 0.3771 0.0261 0.5968 80 K 0.6285 0.0122 0.3593 81 V 0.7972 0.0057 0.1971 82 V 0.8035 0.0055 0.1910 83 V 0.8060 0.0059 0.1881 84 Y 0.7690 0.0091 0.2219 85 D 0.5137 0.0192 0.4671 86 Q 0.2110 0.1916 0.5974 87 S 0.1493 0.1524 0.6982 88 S 0.1457 0.1476 0.7067 89 Q 0.1470 0.2170 0.6360 90 D 0.1828 0.2458 0.5714 91 V 0.0697 0.5434 0.3869 92 A 0.0543 0.5545 0.3912 93 S 0.0626 0.5541 0.3833 94 L 0.0718 0.5413 0.3868 95 S 0.0628 0.5688 0.3684 96 S 0.0400 0.6894 0.2706 97 D 0.0215 0.8110 0.1675 98 C 0.0099 0.8945 0.0956 99 F 0.0086 0.9175 0.0739 100 L 0.0083 0.9227 0.0690 101 T 0.0083 0.9237 0.0680 102 V 0.0083 0.9234 0.0683 103 L 0.0084 0.9189 0.0728 104 L 0.0089 0.9107 0.0803 105 G 0.0093 0.8918 0.0988 106 K 0.0157 0.7936 0.1907 107 L 0.0646 0.3956 0.5398 108 E 0.0614 0.1478 0.7908 109 K 0.1485 0.1359 0.7156 110 S 0.1523 0.1649 0.6828 111 F 0.1897 0.1632 0.6472 112 N 0.2172 0.1684 0.6144 113 S 0.3531 0.0869 0.5600 114 V 0.6265 0.0265 0.3470 115 H 0.7220 0.0234 0.2546 116 L 0.7305 0.0270 0.2425 117 L 0.5361 0.0987 0.3653 118 A 0.2745 0.1941 0.5314 119 G 0.1578 0.2138 0.6284 120 G 0.1314 0.3435 0.5251 121 F 0.0570 0.6706 0.2724 122 A 0.0251 0.8250 0.1500 123 E 0.0197 0.8656 0.1147 124 F 0.0181 0.8528 0.1291 125 S 0.0221 0.8196 0.1582 126 R 0.0314 0.7159 0.2527 127 C 0.0747 0.4076 0.5178 128 F 0.1483 0.1533 0.6984 129 P 0.1132 0.2473 0.6395 130 G 0.1268 0.2582 0.6150 131 L 0.2078 0.2261 0.5660 132 C 0.2679 0.1713 0.5608 133 E 0.2074 0.1430 0.6496 134 G 0.1322 0.1004 0.7673 135 K 0.2244 0.0775 0.6980 136 S 0.2811 0.0951 0.6238 137 T 0.3525 0.0751 0.5724 138 L 0.3325 0.0623 0.6052 139 V 0.3211 0.0335 0.6454 140 P 0.2617 0.1256 0.6127 141 T 0.2417 0.1532 0.6051 142 C 0.2529 0.1454 0.6017 143 I 0.2656 0.1507 0.5837 144 S 0.2528 0.1105 0.6367 145 Q 0.3126 0.0489 0.6386 146 P 0.2602 0.0679 0.6719 147 A 0.2909 0.1606 0.5485 148 H 0.2723 0.1567 0.5710 149 H 0.2666 0.1949 0.5386 150 H 0.2365 0.1949 0.5686 151 H 0.2226 0.1614 0.6161 152 H 0.2181 0.1603 0.6216 153 H 0.2019 0.1407 0.6574