# This file is the result of combining several RDB files, specifically # T0471.t2k.str2.rdb (weight 1.54425) # T0471.t2k.str4.rdb (weight 0.924988) # T0471.t2k.pb.rdb (weight 0.789901) # T0471.t2k.bys.rdb (weight 0.748322) # T0471.t2k.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 T0471.t2k.str2.rdb # ============================================ # TARGET T0471 # Using neural net dunbrack-40pc-3157-t2k-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 T0471.t2k-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 19.0751 # # ============================================ # Comments from T0471.t2k.str4.rdb # ============================================ # TARGET T0471 # Using neural net dunbrack-40pc-3157-t2k-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 T0471.t2k-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 19.0751 # # ============================================ # Comments from T0471.t2k.pb.rdb # ============================================ # TARGET T0471 # Using neural net dunbrack-40pc-3157-t2k-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 T0471.t2k-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 19.0751 # # ============================================ # Comments from T0471.t2k.bys.rdb # ============================================ # TARGET T0471 # Using neural net dunbrack-40pc-3157-t2k-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 T0471.t2k-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 19.0751 # # ============================================ # Comments from T0471.t2k.alpha.rdb # ============================================ # TARGET T0471 # Using neural net dunbrack-40pc-3157-t2k-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 T0471.t2k-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 19.0751 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.1999 0.2751 0.5251 2 W 0.1519 0.3902 0.4580 3 N 0.0971 0.5646 0.3384 4 D 0.0631 0.6896 0.2472 5 L 0.0462 0.7752 0.1786 6 A 0.0511 0.8036 0.1453 7 V 0.0862 0.7776 0.1362 8 Y 0.1554 0.7051 0.1395 9 I 0.2655 0.5899 0.1446 10 I 0.3848 0.4387 0.1765 11 R 0.3806 0.3671 0.2524 12 C 0.3567 0.2675 0.3758 13 S 0.2182 0.1743 0.6075 14 G 0.1621 0.0807 0.7572 15 P 0.1123 0.1748 0.7129 16 G 0.0906 0.1125 0.7969 17 T 0.3110 0.0350 0.6539 18 R 0.5619 0.0201 0.4180 19 V 0.7564 0.0116 0.2320 20 V 0.7633 0.0141 0.2225 21 E 0.7740 0.0070 0.2191 22 V 0.6968 0.0284 0.2748 23 G 0.5153 0.0331 0.4515 24 A 0.3536 0.1137 0.5327 25 G 0.2249 0.1446 0.6304 26 R 0.1705 0.2977 0.5318 27 F 0.1105 0.4887 0.4008 28 L 0.0394 0.7446 0.2160 29 Y 0.0219 0.8456 0.1325 30 V 0.0115 0.8905 0.0980 31 S 0.0084 0.9164 0.0752 32 D 0.0083 0.9209 0.0708 33 Y 0.0085 0.9133 0.0781 34 I 0.0092 0.9051 0.0858 35 R 0.0097 0.8728 0.1175 36 K 0.0175 0.7507 0.2317 37 H 0.0613 0.3947 0.5440 38 S 0.0705 0.1391 0.7904 39 K 0.1980 0.1132 0.6888 40 V 0.3691 0.0943 0.5366 41 D 0.6249 0.0555 0.3196 42 L 0.7441 0.0270 0.2289 43 V 0.7512 0.0227 0.2261 44 L 0.7050 0.0320 0.2630 45 T 0.5490 0.0549 0.3961 46 D 0.3318 0.1463 0.5219 47 I 0.2760 0.1105 0.6135 48 K 0.2084 0.0569 0.7347 49 P 0.1345 0.2078 0.6577 50 S 0.1081 0.2142 0.6777 51 H 0.1306 0.1370 0.7324 52 G 0.1691 0.1033 0.7276 53 G 0.2975 0.0876 0.6148 54 I 0.4855 0.0641 0.4504 55 V 0.5656 0.0784 0.3560 56 R 0.5195 0.1251 0.3554 57 D 0.4309 0.1481 0.4210 58 D 0.3075 0.1994 0.4931 59 I 0.1921 0.2914 0.5165 60 T 0.1717 0.2137 0.6146 61 S 0.1929 0.1308 0.6762 62 P 0.1300 0.2858 0.5842 63 R 0.1705 0.2195 0.6100 64 M 0.2068 0.3602 0.4330 65 E 0.2807 0.4139 0.3054 66 I 0.2643 0.4768 0.2589 67 Y 0.3224 0.2897 0.3879 68 R 0.1784 0.2033 0.6183 69 G 0.1335 0.1151 0.7514 70 A 0.2923 0.0790 0.6288 71 A 0.4631 0.0967 0.4402 72 L 0.7491 0.0440 0.2069 73 I 0.7514 0.0379 0.2107 74 Y 0.7585 0.0307 0.2108 75 S 0.6798 0.0429 0.2774 76 I 0.4805 0.0579 0.4616 77 R 0.3417 0.0307 0.6276 78 P 0.2247 0.0369 0.7384 79 P 0.1345 0.2264 0.6391 80 A 0.0183 0.6995 0.2822 81 E 0.0205 0.7019 0.2776 82 I 0.0338 0.7323 0.2338 83 H 0.0284 0.7602 0.2114 84 S 0.0111 0.8734 0.1155 85 S 0.0099 0.8951 0.0951 86 L 0.0087 0.9057 0.0857 87 M 0.0083 0.9190 0.0726 88 R 0.0083 0.9195 0.0721 89 V 0.0089 0.9046 0.0865 90 A 0.0095 0.8887 0.1017 91 D 0.0120 0.8327 0.1553 92 A 0.0301 0.7182 0.2517 93 V 0.0850 0.2773 0.6377 94 G 0.0773 0.0757 0.8469 95 A 0.2793 0.0344 0.6863 96 R 0.5664 0.0237 0.4099 97 L 0.7861 0.0070 0.2069 98 I 0.7775 0.0072 0.2153 99 I 0.7654 0.0068 0.2278 100 K 0.6743 0.0102 0.3156 101 P 0.4131 0.0457 0.5412 102 L 0.2641 0.1323 0.6035 103 T 0.1522 0.1197 0.7281 104 G 0.1065 0.1226 0.7710 105 E 0.2041 0.1686 0.6274 106 D 0.2986 0.1826 0.5189 107 I 0.3165 0.2239 0.4596 108 V 0.2750 0.2378 0.4872 109 T 0.2353 0.2647 0.5000 110 E 0.1840 0.2617 0.5543 111 R 0.2676 0.1731 0.5592 112 K 0.3761 0.0925 0.5314 113 M 0.4828 0.0949 0.4223 114 K 0.5086 0.0929 0.3985 115 L 0.4894 0.0850 0.4256 116 V 0.3432 0.0920 0.5648 117 N 0.2575 0.1248 0.6177 118 Y 0.2086 0.1259 0.6655 119 G 0.2699 0.1021 0.6280 120 R 0.4461 0.1121 0.4418 121 T 0.6294 0.0823 0.2883 122 Y 0.7097 0.0634 0.2269 123 F 0.7098 0.0855 0.2047 124 Y 0.6469 0.1528 0.2003 125 E 0.5465 0.2658 0.1877 126 Y 0.4688 0.3334 0.1978 127 I 0.3264 0.4744 0.1992 128 A 0.2699 0.5244 0.2057 129 E 0.2328 0.4887 0.2785 130 V 0.2695 0.3855 0.3450 131 R 0.2992 0.2691 0.4318 132 S 0.2214 0.2308 0.5479 133 R 0.1498 0.2211 0.6291