# This file is the result of combining several RDB files, specifically # TR429.t04.str2.rdb (weight 1.54425) # TR429.t04.str4.rdb (weight 0.924988) # TR429.t04.pb.rdb (weight 0.789901) # TR429.t04.bys.rdb (weight 0.748322) # TR429.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 TR429.t04.str2.rdb # ============================================ # TARGET TR429 # 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 TR429.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 5.85934 # # ============================================ # Comments from TR429.t04.str4.rdb # ============================================ # TARGET TR429 # 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 TR429.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 5.85934 # # ============================================ # Comments from TR429.t04.pb.rdb # ============================================ # TARGET TR429 # 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 TR429.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 5.85934 # # ============================================ # Comments from TR429.t04.bys.rdb # ============================================ # TARGET TR429 # 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 TR429.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 5.85934 # # ============================================ # Comments from TR429.t04.alpha.rdb # ============================================ # TARGET TR429 # 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 TR429.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 5.85934 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 E 0.2141 0.0976 0.6883 2 T 0.1600 0.2653 0.5746 3 E 0.1580 0.2501 0.5919 4 L 0.2379 0.1780 0.5841 5 G 0.3080 0.1057 0.5862 6 L 0.5110 0.0748 0.4142 7 Y 0.6107 0.0400 0.3494 8 K 0.5807 0.0346 0.3847 9 V 0.4337 0.1456 0.4206 10 N 0.2679 0.2509 0.4812 11 E 0.2375 0.3063 0.4562 12 Y 0.3235 0.2127 0.4638 13 V 0.4517 0.1059 0.4424 14 D 0.3151 0.0781 0.6068 15 A 0.1729 0.3653 0.4618 16 R 0.1578 0.3737 0.4685 17 D 0.1832 0.3110 0.5058 18 T 0.1333 0.3139 0.5528 19 N 0.1383 0.2472 0.6146 20 M 0.1491 0.1999 0.6510 21 G 0.1964 0.1610 0.6426 22 A 0.4302 0.1701 0.3996 23 W 0.6539 0.1275 0.2186 24 F 0.6780 0.1191 0.2029 25 E 0.6744 0.1506 0.1750 26 A 0.6876 0.1384 0.1740 27 Q 0.6690 0.1491 0.1819 28 V 0.6587 0.1221 0.2192 29 V 0.5915 0.1807 0.2279 30 R 0.6217 0.1235 0.2548 31 V 0.5244 0.1612 0.3144 32 T 0.4536 0.1316 0.4148 33 R 0.3526 0.1642 0.4832 34 K 0.2638 0.1279 0.6083 35 A 0.2337 0.0680 0.6984 36 P 0.1444 0.1963 0.6593 37 S 0.1366 0.2001 0.6632 38 R 0.1344 0.2055 0.6601 39 D 0.1621 0.1365 0.7014 40 E 0.2633 0.0568 0.6799 41 P 0.2614 0.0928 0.6458 42 C 0.2624 0.1364 0.6013 43 S 0.1933 0.1771 0.6296 44 S 0.1656 0.2022 0.6322 45 T 0.1539 0.1885 0.6576 46 S 0.1688 0.1401 0.6911 47 R 0.2392 0.0831 0.6776 48 P 0.2162 0.1685 0.6153 49 A 0.2333 0.1997 0.5670 50 L 0.2199 0.2123 0.5678 51 E 0.1941 0.2714 0.5346 52 E 0.2080 0.2937 0.4983 53 D 0.3597 0.1433 0.4970 54 V 0.6315 0.0350 0.3336 55 I 0.7245 0.0188 0.2567 56 Y 0.7964 0.0086 0.1950 57 H 0.8082 0.0062 0.1855 58 V 0.8059 0.0058 0.1883 59 K 0.7346 0.0105 0.2549 60 Y 0.6056 0.0378 0.3566 61 D 0.3099 0.1622 0.5280 62 D 0.1852 0.1504 0.6643 63 Y 0.2683 0.0509 0.6808 64 P 0.1423 0.2366 0.6211 65 E 0.0900 0.3400 0.5700 66 N 0.1362 0.1577 0.7061 67 G 0.2843 0.0714 0.6443 68 V 0.5841 0.0336 0.3823 69 V 0.7143 0.0219 0.2638 70 Q 0.7480 0.0127 0.2393 71 M 0.7037 0.0232 0.2731 72 N 0.4738 0.0342 0.4920 73 S 0.2321 0.2694 0.4984 74 R 0.1326 0.3395 0.5279 75 D 0.2076 0.1984 0.5941 76 V 0.2916 0.1095 0.5989 77 R 0.2502 0.1026 0.6473 78 A 0.1689 0.4615 0.3695 79 R 0.1497 0.4922 0.3580 80 A 0.1669 0.5629 0.2702 81 R 0.2342 0.4757 0.2901 82 T 0.4500 0.2848 0.2652 83 I 0.4961 0.1839 0.3199 84 I 0.4884 0.1124 0.3992 85 K 0.3297 0.0867 0.5836 86 W 0.1605 0.3955 0.4440 87 Q 0.1256 0.4331 0.4413 88 D 0.2155 0.3042 0.4803 89 L 0.3931 0.0980 0.5089 90 E 0.3684 0.0897 0.5418 91 V 0.2696 0.1017 0.6286 92 G 0.2236 0.0677 0.7087 93 Q 0.5057 0.0230 0.4713 94 V 0.7428 0.0074 0.2498 95 V 0.7791 0.0091 0.2118 96 M 0.7877 0.0082 0.2042 97 L 0.7621 0.0179 0.2200 98 N 0.6333 0.0193 0.3474 99 Y 0.3672 0.0564 0.5764 100 N 0.2354 0.0237 0.7409 101 P 0.0411 0.3924 0.5665 102 D 0.0726 0.2577 0.6698 103 N 0.2061 0.1035 0.6904 104 P 0.1449 0.2503 0.6048 105 K 0.1220 0.3659 0.5121 106 E 0.1746 0.2394 0.5861 107 R 0.2126 0.1338 0.6536 108 G 0.2546 0.0787 0.6668 109 F 0.5174 0.0575 0.4251 110 W 0.6481 0.0517 0.3002 111 Y 0.6891 0.0504 0.2605 112 D 0.6502 0.0652 0.2846 113 A 0.6234 0.1130 0.2636 114 E 0.6270 0.1506 0.2224 115 I 0.5673 0.1631 0.2696 116 S 0.4452 0.2177 0.3371 117 R 0.3668 0.2719 0.3613 118 K 0.2992 0.2755 0.4253 119 R 0.2629 0.2805 0.4566 120 E 0.2569 0.2507 0.4924 121 T 0.2365 0.2068 0.5567 122 R 0.2290 0.2748 0.4962 123 T 0.2468 0.2614 0.4918 124 A 0.1518 0.4963 0.3519 125 R 0.1845 0.4949 0.3206 126 E 0.3602 0.3694 0.2703 127 L 0.5167 0.2124 0.2709 128 Y 0.6393 0.1032 0.2576 129 A 0.7082 0.0585 0.2333 130 N 0.7276 0.0427 0.2298 131 V 0.7609 0.0268 0.2123 132 V 0.7142 0.0318 0.2540 133 L 0.5029 0.0653 0.4317 134 G 0.2605 0.0609 0.6786 135 D 0.1531 0.1804 0.6665 136 D 0.1328 0.2283 0.6389 137 S 0.1864 0.2474 0.5662 138 L 0.1739 0.3231 0.5030 139 N 0.1395 0.3048 0.5557 140 D 0.1736 0.2019 0.6245 141 C 0.3498 0.0752 0.5750 142 R 0.5388 0.0777 0.3834 143 I 0.6884 0.0418 0.2698 144 I 0.6632 0.0549 0.2819 145 F 0.5973 0.0479 0.3548 146 V 0.3031 0.3542 0.3428 147 D 0.2107 0.4877 0.3016 148 E 0.2233 0.5138 0.2630 149 V 0.2906 0.4261 0.2833 150 F 0.3568 0.3655 0.2777 151 K 0.4764 0.2514 0.2722 152 I 0.4800 0.1806 0.3395 153 E 0.3804 0.1177 0.5019 154 R 0.2958 0.0601 0.6441 155 P 0.2016 0.0855 0.7130