# This file is the result of combining several RDB files, specifically # 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) # 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.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 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.1820 0.1698 0.6482 2 S 0.1371 0.2532 0.6097 3 D 0.0994 0.4613 0.4393 4 V 0.0908 0.5597 0.3495 5 I 0.0602 0.6772 0.2626 6 E 0.0420 0.7427 0.2153 7 G 0.0350 0.7651 0.1999 8 R 0.0523 0.7292 0.2185 9 L 0.0662 0.7028 0.2310 10 K 0.0718 0.6879 0.2403 11 E 0.1217 0.5555 0.3228 12 L 0.1907 0.3262 0.4830 13 G 0.2814 0.1725 0.5460 14 F 0.4047 0.1071 0.4882 15 T 0.3543 0.0630 0.5827 16 L 0.2501 0.0591 0.6909 17 P 0.1426 0.2517 0.6057 18 V 0.1487 0.3125 0.5388 19 A 0.1744 0.2549 0.5707 20 A 0.1830 0.1875 0.6295 21 A 0.2102 0.1483 0.6416 22 P 0.1576 0.2275 0.6148 23 A 0.1603 0.2430 0.5967 24 A 0.2061 0.1616 0.6324 25 N 0.1864 0.1732 0.6403 26 Y 0.2473 0.1288 0.6238 27 V 0.3301 0.0672 0.6027 28 P 0.4020 0.1226 0.4754 29 F 0.6283 0.0752 0.2965 30 T 0.7053 0.0448 0.2499 31 I 0.6749 0.0472 0.2780 32 S 0.4685 0.0746 0.4568 33 G 0.2766 0.0617 0.6617 34 N 0.3054 0.0696 0.6250 35 L 0.6468 0.0218 0.3313 36 L 0.7375 0.0165 0.2460 37 Y 0.7647 0.0101 0.2252 38 V 0.7207 0.0268 0.2524 39 S 0.5483 0.0526 0.3992 40 G 0.3585 0.0623 0.5792 41 Q 0.3642 0.0623 0.5735 42 L 0.3808 0.0397 0.5796 43 P 0.2953 0.0568 0.6479 44 M 0.2819 0.1195 0.5986 45 E 0.2319 0.0684 0.6997 46 S 0.0916 0.2691 0.6394 47 G 0.0614 0.1886 0.7500 48 K 0.2621 0.1216 0.6164 49 I 0.4823 0.0889 0.4288 50 A 0.5268 0.1208 0.3524 51 V 0.4969 0.1282 0.3749 52 T 0.4235 0.0958 0.4806 53 G 0.3749 0.0713 0.5538 54 L 0.4573 0.0725 0.4702 55 V 0.4485 0.0767 0.4748 56 G 0.2960 0.0773 0.6267 57 R 0.1621 0.2075 0.6304 58 D 0.1393 0.1432 0.7175 59 V 0.2548 0.0756 0.6696 60 D 0.2206 0.0396 0.7398 61 V 0.0416 0.5752 0.3833 62 A 0.0186 0.7293 0.2520 63 S 0.0226 0.7954 0.1820 64 A 0.0094 0.9019 0.0887 65 Q 0.0084 0.9200 0.0716 66 R 0.0083 0.9246 0.0672 67 A 0.0083 0.9240 0.0677 68 A 0.0083 0.9241 0.0676 69 E 0.0083 0.9248 0.0669 70 L 0.0083 0.9229 0.0688 71 C 0.0083 0.9216 0.0701 72 A 0.0083 0.9228 0.0689 73 V 0.0084 0.9238 0.0678 74 N 0.0085 0.9166 0.0748 75 I 0.0084 0.9202 0.0715 76 L 0.0083 0.9241 0.0676 77 A 0.0083 0.9248 0.0670 78 Q 0.0083 0.9240 0.0677 79 V 0.0083 0.9213 0.0704 80 K 0.0084 0.9178 0.0738 81 A 0.0089 0.8907 0.1005 82 A 0.0146 0.7774 0.2080 83 L 0.0310 0.6184 0.3506 84 N 0.0549 0.2373 0.7078 85 G 0.0543 0.1553 0.7904 86 D 0.1233 0.1665 0.7101 87 L 0.0578 0.5082 0.4340 88 S 0.0470 0.5782 0.3748 89 K 0.0631 0.6186 0.3183 90 I 0.0424 0.6922 0.2654 91 R 0.0325 0.7518 0.2157 92 R 0.0678 0.6530 0.2792 93 V 0.2374 0.4292 0.3335 94 I 0.3747 0.3137 0.3115 95 K 0.5822 0.1545 0.2632 96 L 0.6438 0.0696 0.2866 97 N 0.6614 0.0532 0.2855 98 G 0.6913 0.0461 0.2627 99 F 0.6970 0.0505 0.2525 100 V 0.6131 0.0806 0.3063 101 A 0.4499 0.1183 0.4318 102 S 0.2259 0.0828 0.6913 103 V 0.1057 0.3134 0.5810 104 P 0.0288 0.5699 0.4013 105 E 0.0238 0.6930 0.2832 106 F 0.0359 0.6808 0.2834 107 V 0.0307 0.6858 0.2835 108 E 0.0350 0.6154 0.3496 109 Q 0.0690 0.5517 0.3794 110 H 0.0743 0.5590 0.3668 111 L 0.0694 0.6690 0.2617 112 V 0.1117 0.6259 0.2624 113 I 0.1343 0.5314 0.3343 114 N 0.0899 0.4662 0.4438 115 G 0.0539 0.5887 0.3574 116 A 0.0284 0.7930 0.1786 117 S 0.0132 0.8820 0.1048 118 N 0.0117 0.9060 0.0824 119 L 0.0100 0.9153 0.0747 120 I 0.0098 0.9088 0.0813 121 A 0.0100 0.9045 0.0855 122 T 0.0150 0.8674 0.1175 123 V 0.0377 0.6982 0.2640 124 L 0.0852 0.3413 0.5734 125 G 0.0787 0.1847 0.7365 126 E 0.1404 0.1294 0.7302 127 P 0.1019 0.2142 0.6838 128 G 0.0773 0.1390 0.7838 129 R 0.1609 0.1215 0.7175 130 H 0.2284 0.1249 0.6466 131 A 0.2282 0.3556 0.4162 132 R 0.2907 0.3989 0.3105 133 A 0.4033 0.3332 0.2635 134 A 0.4833 0.2576 0.2591 135 V 0.5624 0.1949 0.2427 136 G 0.4850 0.2240 0.2910 137 M 0.3283 0.3368 0.3349 138 A 0.2384 0.3480 0.4136 139 S 0.2351 0.2329 0.5319 140 L 0.2378 0.0792 0.6830 141 P 0.1816 0.0952 0.7232 142 F 0.1095 0.2040 0.6865 143 N 0.0925 0.1026 0.8049 144 A 0.3099 0.0334 0.6568 145 S 0.5913 0.0202 0.3886 146 V 0.7783 0.0061 0.2156 147 E 0.8038 0.0065 0.1897 148 I 0.8213 0.0041 0.1746 149 D 0.8129 0.0072 0.1800 150 A 0.8189 0.0042 0.1769 151 I 0.8252 0.0052 0.1696 152 V 0.8067 0.0057 0.1876 153 E 0.7826 0.0097 0.2077 154 I 0.6749 0.0165 0.3086 155 D 0.4744 0.0289 0.4967 156 V 0.3383 0.0852 0.5764