# This file is the result of combining several RDB files, specifically # T0429.t04.str2.rdb (weight 1.54425) # T0429.t04.str4.rdb (weight 0.924988) # T0429.t04.pb.rdb (weight 0.789901) # T0429.t04.bys.rdb (weight 0.748322) # T0429.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 T0429.t04.str2.rdb # ============================================ # TARGET T0429 # 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 T0429.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 8.69522 # # ============================================ # Comments from T0429.t04.str4.rdb # ============================================ # TARGET T0429 # 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 T0429.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 8.69522 # # ============================================ # Comments from T0429.t04.pb.rdb # ============================================ # TARGET T0429 # 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 T0429.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 8.69522 # # ============================================ # Comments from T0429.t04.bys.rdb # ============================================ # TARGET T0429 # 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 T0429.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 8.69522 # # ============================================ # Comments from T0429.t04.alpha.rdb # ============================================ # TARGET T0429 # 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 T0429.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 8.69522 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.2296 0.1244 0.6459 2 H 0.2055 0.1288 0.6657 3 H 0.2364 0.1424 0.6212 4 H 0.2237 0.1677 0.6086 5 H 0.2263 0.1653 0.6085 6 H 0.2265 0.1457 0.6277 7 H 0.1990 0.1477 0.6532 8 S 0.1657 0.2220 0.6123 9 S 0.1448 0.2062 0.6490 10 G 0.1310 0.1404 0.7286 11 R 0.2253 0.1361 0.6386 12 E 0.2058 0.2763 0.5179 13 N 0.2253 0.2473 0.5274 14 L 0.2340 0.2914 0.4747 15 Y 0.2434 0.2804 0.4762 16 F 0.2063 0.3008 0.4929 17 Q 0.1834 0.2482 0.5684 18 G 0.1780 0.2169 0.6051 19 M 0.2855 0.1886 0.5259 20 W 0.3205 0.1930 0.4864 21 D 0.2677 0.2375 0.4948 22 E 0.2491 0.2168 0.5341 23 T 0.1499 0.3303 0.5198 24 E 0.1385 0.2773 0.5843 25 L 0.2267 0.1636 0.6097 26 G 0.3258 0.1092 0.5650 27 L 0.5151 0.0934 0.3916 28 Y 0.6192 0.0466 0.3342 29 K 0.6031 0.0425 0.3544 30 V 0.4736 0.1545 0.3719 31 N 0.3203 0.2520 0.4277 32 E 0.3244 0.2824 0.3932 33 Y 0.4317 0.1690 0.3993 34 V 0.5314 0.0828 0.3858 35 D 0.4027 0.0641 0.5332 36 A 0.2360 0.3435 0.4205 37 R 0.2123 0.3620 0.4258 38 D 0.2160 0.2734 0.5105 39 T 0.1505 0.2907 0.5587 40 N 0.1414 0.2342 0.6244 41 M 0.1323 0.1919 0.6759 42 G 0.1479 0.1483 0.7038 43 A 0.3414 0.1400 0.5186 44 W 0.5799 0.1030 0.3171 45 F 0.6234 0.0991 0.2775 46 E 0.6138 0.1264 0.2598 47 A 0.6376 0.1137 0.2487 48 Q 0.6458 0.1092 0.2450 49 V 0.6601 0.0816 0.2583 50 V 0.6328 0.0976 0.2696 51 R 0.6886 0.0566 0.2548 52 V 0.6023 0.0760 0.3217 53 T 0.5014 0.0746 0.4239 54 R 0.3828 0.1277 0.4896 55 K 0.2791 0.1184 0.6025 56 A 0.2432 0.0620 0.6948 57 P 0.1519 0.1871 0.6611 58 S 0.1498 0.1839 0.6663 59 R 0.1344 0.2118 0.6538 60 D 0.1646 0.1347 0.7007 61 E 0.2834 0.0454 0.6712 62 P 0.2895 0.0694 0.6411 63 C 0.2749 0.1183 0.6068 64 S 0.1894 0.1711 0.6395 65 S 0.1605 0.1883 0.6512 66 T 0.1530 0.1815 0.6655 67 S 0.1705 0.1283 0.7012 68 R 0.2445 0.0700 0.6856 69 P 0.2048 0.1787 0.6164 70 A 0.2195 0.2357 0.5448 71 L 0.2255 0.2211 0.5535 72 E 0.2105 0.2529 0.5367 73 E 0.2775 0.1951 0.5274 74 D 0.4175 0.0877 0.4948 75 V 0.6674 0.0188 0.3138 76 I 0.7521 0.0103 0.2376 77 Y 0.8080 0.0055 0.1865 78 H 0.8132 0.0051 0.1817 79 V 0.8024 0.0056 0.1920 80 K 0.7187 0.0097 0.2715 81 Y 0.5534 0.0363 0.4103 82 D 0.2766 0.1524 0.5711 83 D 0.1850 0.1417 0.6733 84 Y 0.2723 0.0439 0.6838 85 P 0.1623 0.2008 0.6370 86 E 0.1035 0.3195 0.5770 87 N 0.1299 0.1495 0.7207 88 G 0.2493 0.0668 0.6839 89 V 0.5675 0.0268 0.4057 90 V 0.7070 0.0201 0.2729 91 Q 0.7402 0.0111 0.2487 92 M 0.6884 0.0221 0.2895 93 N 0.4362 0.0302 0.5336 94 S 0.2112 0.2808 0.5080 95 R 0.1221 0.3779 0.5001 96 D 0.2134 0.2352 0.5515 97 V 0.3038 0.1313 0.5649 98 R 0.2507 0.1221 0.6272 99 A 0.1594 0.4932 0.3474 100 R 0.1437 0.5213 0.3350 101 A 0.1599 0.5872 0.2529 102 R 0.2183 0.5167 0.2649 103 T 0.4306 0.3260 0.2434 104 I 0.4969 0.2062 0.2969 105 I 0.4908 0.1326 0.3766 106 K 0.3498 0.1079 0.5422 107 W 0.1910 0.3529 0.4561 108 Q 0.1418 0.3445 0.5138 109 D 0.2162 0.1961 0.5877 110 L 0.3863 0.0445 0.5692 111 E 0.3752 0.0453 0.5795 112 V 0.3096 0.0868 0.6037 113 G 0.2603 0.0666 0.6732 114 Q 0.5705 0.0178 0.4117 115 V 0.7437 0.0068 0.2494 116 V 0.7815 0.0096 0.2089 117 M 0.7875 0.0076 0.2049 118 L 0.7643 0.0181 0.2176 119 N 0.6637 0.0162 0.3201 120 Y 0.4073 0.0490 0.5438 121 N 0.2404 0.0225 0.7371 122 P 0.0470 0.3643 0.5887 123 D 0.0791 0.2368 0.6840 124 N 0.2137 0.0884 0.6979 125 P 0.1588 0.2242 0.6170 126 K 0.1469 0.3384 0.5147 127 E 0.2179 0.2197 0.5624 128 R 0.2353 0.1351 0.6296 129 G 0.2597 0.0848 0.6555 130 F 0.5068 0.0676 0.4256 131 W 0.6290 0.0632 0.3078 132 Y 0.6766 0.0592 0.2642 133 D 0.6379 0.0754 0.2867 134 A 0.6245 0.1104 0.2651 135 E 0.6431 0.1383 0.2186 136 I 0.5979 0.1411 0.2610 137 S 0.4901 0.1925 0.3174 138 R 0.3605 0.3035 0.3360 139 K 0.2508 0.3454 0.4038 140 R 0.2084 0.3593 0.4323 141 E 0.2268 0.2952 0.4780 142 T 0.2343 0.2485 0.5172 143 R 0.2428 0.2818 0.4755 144 T 0.2599 0.2604 0.4797 145 A 0.1603 0.4995 0.3402 146 R 0.2010 0.4926 0.3063 147 E 0.3904 0.3507 0.2589 148 L 0.5407 0.1950 0.2644 149 Y 0.6709 0.0806 0.2485 150 A 0.7332 0.0420 0.2248 151 N 0.7523 0.0290 0.2187 152 V 0.7768 0.0178 0.2054 153 V 0.7347 0.0230 0.2423 154 L 0.5372 0.0555 0.4073 155 G 0.2767 0.0559 0.6674 156 D 0.1538 0.1799 0.6663 157 D 0.1297 0.2208 0.6495 158 S 0.1802 0.2483 0.5715 159 L 0.1656 0.3399 0.4946 160 N 0.1319 0.3232 0.5449 161 D 0.1662 0.2079 0.6259 162 C 0.3438 0.0746 0.5816 163 R 0.5252 0.0776 0.3973 164 I 0.6847 0.0400 0.2753 165 I 0.6621 0.0525 0.2854 166 F 0.6121 0.0416 0.3463 167 V 0.3303 0.3265 0.3432 168 D 0.2605 0.4306 0.3090 169 E 0.2869 0.4413 0.2718 170 V 0.3547 0.3556 0.2898 171 F 0.4636 0.2617 0.2747 172 K 0.5898 0.1626 0.2476 173 I 0.5511 0.1305 0.3184 174 E 0.4330 0.1083 0.4587 175 R 0.2888 0.0473 0.6639 176 P 0.1675 0.1287 0.7038 177 G 0.1040 0.1061 0.7899 178 E 0.1706 0.1160 0.7135