# This file is the result of combining several RDB files, specifically # TR429.t06.str2.rdb (weight 1.54425) # TR429.t06.str4.rdb (weight 0.924988) # TR429.t06.pb.rdb (weight 0.789901) # TR429.t06.bys.rdb (weight 0.748322) # TR429.t06.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 TR429.t06.str2.rdb # ============================================ # TARGET TR429 # 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 TR429.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 5.80399 # # ============================================ # Comments from TR429.t06.str4.rdb # ============================================ # TARGET TR429 # 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 TR429.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 5.80399 # # ============================================ # Comments from TR429.t06.pb.rdb # ============================================ # TARGET TR429 # 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 TR429.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 5.80399 # # ============================================ # Comments from TR429.t06.bys.rdb # ============================================ # TARGET TR429 # 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 TR429.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 5.80399 # # ============================================ # Comments from TR429.t06.alpha.rdb # ============================================ # TARGET TR429 # 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 TR429.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 5.80399 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 E 0.2050 0.1092 0.6858 2 T 0.1686 0.2148 0.6166 3 E 0.1709 0.2373 0.5918 4 L 0.2565 0.1672 0.5763 5 G 0.3234 0.1123 0.5643 6 L 0.5469 0.0790 0.3741 7 Y 0.5925 0.0616 0.3459 8 K 0.5566 0.0671 0.3763 9 V 0.3856 0.1392 0.4752 10 N 0.2978 0.1584 0.5438 11 E 0.3250 0.2095 0.4655 12 Y 0.4525 0.1425 0.4050 13 V 0.5176 0.0706 0.4118 14 D 0.3422 0.0782 0.5796 15 A 0.1574 0.3837 0.4589 16 R 0.1260 0.3930 0.4810 17 D 0.1724 0.3130 0.5146 18 T 0.1291 0.3298 0.5411 19 N 0.1564 0.2534 0.5902 20 M 0.1698 0.2062 0.6240 21 G 0.2203 0.1423 0.6373 22 A 0.5512 0.1068 0.3419 23 W 0.6788 0.0796 0.2416 24 F 0.6872 0.1106 0.2022 25 E 0.6883 0.1077 0.2040 26 A 0.7420 0.0642 0.1937 27 Q 0.7097 0.0835 0.2068 28 V 0.6752 0.0940 0.2308 29 V 0.5851 0.1323 0.2827 30 R 0.5942 0.1327 0.2731 31 V 0.5476 0.1304 0.3220 32 T 0.4899 0.1394 0.3707 33 R 0.3298 0.1796 0.4906 34 K 0.2550 0.1503 0.5947 35 A 0.2289 0.0603 0.7108 36 P 0.1534 0.1777 0.6689 37 S 0.1405 0.1800 0.6795 38 R 0.1333 0.2082 0.6586 39 D 0.1524 0.1344 0.7132 40 E 0.2341 0.0606 0.7052 41 P 0.2243 0.1035 0.6722 42 C 0.2232 0.1435 0.6332 43 S 0.1848 0.1853 0.6300 44 S 0.1514 0.2201 0.6286 45 T 0.1417 0.2246 0.6337 46 S 0.1632 0.1533 0.6835 47 R 0.2143 0.0966 0.6890 48 P 0.1720 0.1980 0.6299 49 A 0.2019 0.2242 0.5740 50 L 0.1957 0.2402 0.5641 51 E 0.1663 0.3267 0.5070 52 E 0.2318 0.2680 0.5002 53 D 0.4139 0.1082 0.4779 54 V 0.6988 0.0299 0.2714 55 I 0.7451 0.0163 0.2386 56 Y 0.8106 0.0077 0.1817 57 H 0.8038 0.0065 0.1897 58 V 0.8049 0.0063 0.1888 59 K 0.7644 0.0103 0.2252 60 Y 0.6135 0.0379 0.3485 61 D 0.3389 0.1326 0.5285 62 D 0.2179 0.1352 0.6469 63 Y 0.2737 0.0540 0.6723 64 P 0.1347 0.2635 0.6018 65 E 0.0746 0.3355 0.5899 66 N 0.0977 0.1811 0.7212 67 G 0.2207 0.0887 0.6907 68 V 0.5549 0.0303 0.4148 69 V 0.6971 0.0230 0.2798 70 Q 0.7209 0.0185 0.2606 71 M 0.6710 0.0207 0.3083 72 N 0.4380 0.0324 0.5297 73 S 0.2440 0.2130 0.5430 74 R 0.1379 0.3414 0.5207 75 D 0.1737 0.2304 0.5959 76 V 0.2820 0.1507 0.5673 77 R 0.2779 0.1246 0.5975 78 A 0.1627 0.4493 0.3880 79 R 0.0919 0.6110 0.2970 80 A 0.1475 0.5954 0.2571 81 R 0.1875 0.5356 0.2769 82 T 0.2596 0.4763 0.2641 83 I 0.3291 0.3225 0.3485 84 I 0.4178 0.1835 0.3986 85 K 0.3166 0.1348 0.5486 86 W 0.1535 0.3730 0.4735 87 Q 0.1102 0.4285 0.4613 88 D 0.1499 0.3438 0.5063 89 L 0.2966 0.1530 0.5504 90 E 0.2982 0.1056 0.5962 91 V 0.2249 0.1438 0.6313 92 G 0.1926 0.0872 0.7201 93 Q 0.4948 0.0322 0.4730 94 V 0.7402 0.0096 0.2503 95 V 0.7891 0.0096 0.2013 96 M 0.7993 0.0073 0.1934 97 L 0.7637 0.0150 0.2213 98 N 0.6233 0.0275 0.3492 99 Y 0.4587 0.0428 0.4985 100 N 0.2608 0.0243 0.7149 101 P 0.0517 0.3888 0.5596 102 D 0.0548 0.3144 0.6308 103 N 0.1326 0.2051 0.6623 104 P 0.0956 0.3752 0.5292 105 K 0.0905 0.4031 0.5063 106 E 0.1289 0.3297 0.5414 107 R 0.2028 0.1540 0.6432 108 G 0.3008 0.0844 0.6148 109 F 0.5825 0.0451 0.3723 110 W 0.7023 0.0450 0.2527 111 Y 0.6697 0.0729 0.2575 112 D 0.6100 0.0946 0.2955 113 A 0.5899 0.1930 0.2171 114 E 0.6090 0.1784 0.2126 115 I 0.5799 0.1932 0.2269 116 S 0.4229 0.2833 0.2939 117 R 0.3685 0.2710 0.3605 118 K 0.3128 0.2666 0.4206 119 R 0.2535 0.2861 0.4604 120 E 0.2006 0.2872 0.5122 121 T 0.2040 0.2603 0.5357 122 R 0.1944 0.2785 0.5271 123 T 0.2485 0.2467 0.5048 124 A 0.1813 0.4366 0.3821 125 R 0.2202 0.4392 0.3406 126 E 0.4462 0.2620 0.2919 127 L 0.5818 0.1315 0.2867 128 Y 0.6759 0.0797 0.2445 129 A 0.7499 0.0427 0.2073 130 N 0.7405 0.0384 0.2211 131 V 0.7687 0.0243 0.2070 132 V 0.7009 0.0392 0.2599 133 L 0.5598 0.0487 0.3915 134 G 0.2496 0.0547 0.6957 135 D 0.1543 0.1854 0.6602 136 D 0.1295 0.2273 0.6432 137 S 0.1754 0.2510 0.5735 138 L 0.1861 0.2467 0.5672 139 N 0.1498 0.2330 0.6173 140 D 0.1813 0.1753 0.6434 141 C 0.3689 0.0856 0.5455 142 R 0.5655 0.0555 0.3790 143 I 0.7144 0.0302 0.2554 144 I 0.6998 0.0400 0.2602 145 F 0.6391 0.0530 0.3079 146 V 0.4326 0.2280 0.3394 147 D 0.3511 0.3330 0.3159 148 E 0.4126 0.3118 0.2756 149 V 0.5408 0.1936 0.2656 150 F 0.5957 0.1234 0.2810 151 K 0.6503 0.0815 0.2682 152 I 0.6128 0.0615 0.3258 153 E 0.5431 0.0596 0.3974 154 R 0.3882 0.0341 0.5778 155 P 0.2287 0.0883 0.6830