# This file is the result of combining several RDB files, specifically # T0407.t06.str2.rdb (weight 1.54425) # T0407.t06.str4.rdb (weight 0.924988) # T0407.t06.pb.rdb (weight 0.789901) # T0407.t06.bys.rdb (weight 0.748322) # T0407.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 T0407.t06.str2.rdb # ============================================ # TARGET T0407 # 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 T0407.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 6.03924 # # ============================================ # Comments from T0407.t06.str4.rdb # ============================================ # TARGET T0407 # 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 T0407.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 6.03924 # # ============================================ # Comments from T0407.t06.pb.rdb # ============================================ # TARGET T0407 # 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 T0407.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 6.03924 # # ============================================ # Comments from T0407.t06.bys.rdb # ============================================ # TARGET T0407 # 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 T0407.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 6.03924 # # ============================================ # Comments from T0407.t06.alpha.rdb # ============================================ # TARGET T0407 # 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 T0407.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 6.03924 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 I 0.3803 0.0602 0.5595 2 Q 0.3525 0.0664 0.5812 3 T 0.3689 0.1075 0.5236 4 D 0.3180 0.1625 0.5196 5 Y 0.3754 0.1190 0.5057 6 D 0.3202 0.1102 0.5696 7 F 0.2300 0.2526 0.5174 8 E 0.1565 0.3001 0.5434 9 K 0.1289 0.1959 0.6752 10 G 0.1065 0.0960 0.7975 11 E 0.2445 0.0914 0.6641 12 H 0.4178 0.0478 0.5344 13 R 0.4962 0.0298 0.4739 14 T 0.5728 0.0258 0.4014 15 M 0.6302 0.0309 0.3389 16 T 0.6953 0.0399 0.2647 17 F 0.6952 0.1047 0.2000 18 V 0.5949 0.1998 0.2053 19 F 0.5134 0.2537 0.2329 20 A 0.3295 0.4325 0.2379 21 K 0.1678 0.5510 0.2812 22 E 0.1152 0.5245 0.3603 23 R 0.1123 0.4049 0.4828 24 S 0.1256 0.2993 0.5751 25 L 0.0142 0.7759 0.2099 26 Q 0.0094 0.8666 0.1239 27 G 0.0088 0.9133 0.0780 28 I 0.0084 0.9152 0.0764 29 R 0.0084 0.9172 0.0744 30 E 0.0083 0.9164 0.0753 31 A 0.0090 0.8980 0.0930 32 L 0.0112 0.8709 0.1178 33 D 0.0149 0.7165 0.2686 34 N 0.0290 0.4735 0.4975 35 R 0.0711 0.2550 0.6739 36 R 0.2093 0.1567 0.6340 37 T 0.3808 0.1521 0.4671 38 A 0.4899 0.2560 0.2541 39 A 0.5575 0.2361 0.2064 40 Y 0.5471 0.2314 0.2215 41 F 0.3130 0.4185 0.2685 42 H 0.1278 0.5950 0.2772 43 E 0.0959 0.6280 0.2761 44 L 0.1071 0.6142 0.2786 45 L 0.1517 0.4783 0.3700 46 I 0.1569 0.3007 0.5424 47 G 0.1345 0.2102 0.6553 48 R 0.0776 0.4815 0.4409 49 E 0.0191 0.7571 0.2238 50 D 0.0116 0.8066 0.1819 51 L 0.0149 0.7998 0.1853 52 L 0.0243 0.7583 0.2174 53 R 0.0170 0.8055 0.1774 54 P 0.0102 0.8658 0.1241 55 F 0.0113 0.8483 0.1405 56 F 0.0183 0.8333 0.1484 57 E 0.0266 0.7626 0.2109 58 K 0.0546 0.5882 0.3572 59 C 0.1999 0.3088 0.4913 60 V 0.4707 0.1199 0.4095 61 K 0.6202 0.0575 0.3223 62 I 0.5808 0.0603 0.3589 63 E 0.5157 0.0968 0.3875 64 E 0.6044 0.0704 0.3251 65 V 0.5313 0.0726 0.3961 66 S 0.4140 0.0711 0.5149 67 R 0.2237 0.2132 0.5631 68 N 0.1613 0.1894 0.6493 69 E 0.1831 0.1776 0.6392 70 Q 0.2154 0.1267 0.6579 71 G 0.3090 0.0614 0.6296 72 V 0.5662 0.0120 0.4218 73 T 0.6876 0.0094 0.3030 74 L 0.7571 0.0077 0.2351 75 S 0.7578 0.0109 0.2313 76 I 0.7138 0.0149 0.2713 77 T 0.5637 0.0356 0.4007 78 N 0.3268 0.0308 0.6424 79 V 0.1576 0.2691 0.5732 80 T 0.1794 0.3518 0.4689 81 D 0.2654 0.2958 0.4387 82 L 0.3653 0.3361 0.2986 83 V 0.3825 0.3747 0.2429 84 L 0.4581 0.3097 0.2322 85 K 0.4477 0.2927 0.2596 86 L 0.3854 0.2391 0.3755 87 K 0.2127 0.2634 0.5239 88 K 0.1363 0.2828 0.5809 89 T 0.1505 0.2530 0.5965 90 A 0.1546 0.2680 0.5774 91 H 0.1494 0.2851 0.5655 92 D 0.1618 0.2696 0.5686 93 T 0.2226 0.2654 0.5120 94 L 0.3158 0.2267 0.4575 95 L 0.4198 0.1758 0.4044 96 V 0.5114 0.1227 0.3659 97 Y 0.4369 0.1042 0.4590 98 F 0.3327 0.1878 0.4795 99 R 0.2828 0.2178 0.4995 100 D 0.3997 0.1347 0.4656 101 M 0.5757 0.0457 0.3786 102 T 0.6024 0.0312 0.3664 103 L 0.5170 0.0249 0.4580 104 K 0.2483 0.0201 0.7316 105 P 0.1365 0.2672 0.5963 106 H 0.1173 0.1597 0.7230 107 T 0.3214 0.0840 0.5945 108 R 0.5141 0.0302 0.4557 109 Y 0.6960 0.0175 0.2865 110 T 0.7678 0.0079 0.2243 111 V 0.8096 0.0056 0.1848 112 R 0.7907 0.0071 0.2022 113 I 0.7678 0.0095 0.2227 114 G 0.6650 0.0217 0.3133 115 F 0.4756 0.0641 0.4603 116 K 0.2763 0.2210 0.5027 117 Q 0.1742 0.2478 0.5780 118 G 0.1365 0.1723 0.6912 119 I 0.2479 0.0834 0.6687 120 K 0.2104 0.1327 0.6570 121 G 0.2285 0.1089 0.6626 122 G 0.3635 0.0860 0.5505 123 D 0.5227 0.0529 0.4244 124 V 0.5848 0.0482 0.3670 125 N 0.5388 0.0824 0.3789 126 F 0.6514 0.0492 0.2993 127 E 0.6949 0.0580 0.2471 128 V 0.6744 0.0566 0.2689 129 T 0.5148 0.1138 0.3714 130 N 0.4849 0.0481 0.4671 131 F 0.6396 0.0270 0.3334 132 I 0.7057 0.0273 0.2670 133 V 0.6712 0.0270 0.3018 134 A 0.4710 0.0232 0.5058 135 P 0.2449 0.1206 0.6344 136 D 0.1539 0.1756 0.6705 137 K 0.1078 0.2521 0.6401 138 G 0.0839 0.1698 0.7463 139 L 0.3223 0.0426 0.6350 140 K 0.5037 0.0249 0.4714 141 Y 0.6830 0.0145 0.3025 142 T 0.7184 0.0132 0.2683 143 I 0.7527 0.0118 0.2355 144 S 0.6298 0.0184 0.3519 145 L 0.4367 0.0658 0.4975