# This file is the result of combining several RDB files, specifically # T0514.t04.str2.rdb (weight 1.54425) # T0514.t04.str4.rdb (weight 0.924988) # T0514.t04.pb.rdb (weight 0.789901) # T0514.t04.bys.rdb (weight 0.748322) # T0514.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 T0514.t04.str2.rdb # ============================================ # TARGET T0514 # 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 T0514.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 202 # # ============================================ # Comments from T0514.t04.str4.rdb # ============================================ # TARGET T0514 # 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 T0514.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 202 # # ============================================ # Comments from T0514.t04.pb.rdb # ============================================ # TARGET T0514 # 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 T0514.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 202 # # ============================================ # Comments from T0514.t04.bys.rdb # ============================================ # TARGET T0514 # 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 T0514.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 202 # # ============================================ # Comments from T0514.t04.alpha.rdb # ============================================ # TARGET T0514 # 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 T0514.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 202 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 S 0.2318 0.1249 0.6433 2 S 0.3100 0.1224 0.5676 3 L 0.3865 0.1377 0.4758 4 T 0.4051 0.1494 0.4455 5 E 0.4378 0.1318 0.4305 6 T 0.3931 0.1216 0.4853 7 Y 0.2741 0.0972 0.6286 8 G 0.2134 0.0889 0.6977 9 L 0.3846 0.0898 0.5256 10 W 0.6222 0.0556 0.3223 11 S 0.7513 0.0228 0.2259 12 I 0.7846 0.0183 0.1971 13 N 0.7336 0.0296 0.2368 14 C 0.7017 0.0326 0.2657 15 G 0.5902 0.0663 0.3435 16 I 0.5462 0.0744 0.3794 17 Q 0.3845 0.0987 0.5168 18 E 0.1287 0.1709 0.7003 19 G 0.0645 0.1169 0.8186 20 K 0.2532 0.0523 0.6945 21 K 0.4862 0.0415 0.4723 22 V 0.6868 0.0313 0.2819 23 C 0.7482 0.0225 0.2293 24 F 0.7723 0.0241 0.2036 25 M 0.7642 0.0283 0.2075 26 H 0.7158 0.0471 0.2371 27 R 0.6782 0.0483 0.2735 28 Q 0.6280 0.0578 0.3142 29 E 0.5390 0.0864 0.3746 30 V 0.4319 0.0971 0.4710 31 N 0.2284 0.1362 0.6354 32 D 0.1161 0.2873 0.5966 33 Q 0.0891 0.1888 0.7221 34 N 0.1000 0.0997 0.8003 35 R 0.3484 0.0250 0.6267 36 V 0.6465 0.0182 0.3353 37 V 0.7836 0.0098 0.2067 38 V 0.8168 0.0066 0.1766 39 A 0.8218 0.0043 0.1740 40 M 0.8300 0.0043 0.1657 41 S 0.8270 0.0043 0.1687 42 V 0.8259 0.0049 0.1692 43 V 0.8008 0.0074 0.1918 44 L 0.7200 0.0194 0.2606 45 N 0.4004 0.0190 0.5805 46 A 0.1212 0.2799 0.5989 47 D 0.0748 0.1617 0.7634 48 G 0.0729 0.1033 0.8238 49 V 0.3433 0.0255 0.6312 50 V 0.5979 0.0255 0.3767 51 S 0.6069 0.0317 0.3615 52 G 0.7008 0.0155 0.2838 53 N 0.7407 0.0096 0.2497 54 L 0.7755 0.0067 0.2178 55 T 0.7736 0.0105 0.2159 56 V 0.6965 0.0111 0.2924 57 P 0.5090 0.0293 0.4617 58 F 0.3297 0.1139 0.5564 59 G 0.2523 0.0936 0.6541 60 I 0.4433 0.0579 0.4988 61 L 0.5151 0.0486 0.4363 62 V 0.4621 0.0535 0.4844 63 S 0.3481 0.0436 0.6083 64 K 0.3185 0.0701 0.6113 65 P 0.3877 0.0383 0.5740 66 V 0.6283 0.0134 0.3583 67 R 0.7401 0.0078 0.2521 68 L 0.7974 0.0050 0.1975 69 Q 0.7589 0.0068 0.2343 70 V 0.6712 0.0154 0.3134 71 D 0.3131 0.0583 0.6286 72 E 0.1453 0.1222 0.7325 73 G 0.1159 0.1065 0.7776 74 K 0.3074 0.0868 0.6058 75 A 0.4723 0.1063 0.4214 76 V 0.5188 0.1187 0.3625 77 I 0.5640 0.1120 0.3240 78 E 0.4926 0.1292 0.3782 79 T 0.4481 0.0839 0.4680 80 G 0.3668 0.0914 0.5419 81 I 0.4628 0.0956 0.4417 82 R 0.5293 0.0931 0.3776 83 T 0.5758 0.0694 0.3547 84 C 0.4690 0.0671 0.4638 85 V 0.3244 0.0598 0.6158 86 P 0.2037 0.1534 0.6429 87 A 0.1564 0.1633 0.6803 88 G 0.2291 0.0934 0.6775 89 C 0.4377 0.0649 0.4974 90 I 0.6002 0.0544 0.3454 91 V 0.6462 0.0291 0.3247 92 P 0.5518 0.0635 0.3847 93 I 0.5179 0.0852 0.3969 94 V 0.3612 0.1304 0.5084 95 F 0.2739 0.1161 0.6100 96 D 0.1699 0.1276 0.7025 97 K 0.0109 0.7555 0.2336 98 N 0.0095 0.8683 0.1222 99 Y 0.0085 0.9172 0.0743 100 V 0.0083 0.9229 0.0688 101 A 0.0083 0.9229 0.0688 102 A 0.0084 0.9203 0.0713 103 L 0.0093 0.9061 0.0846 104 R 0.0126 0.8216 0.1658 105 A 0.0479 0.3463 0.6057 106 G 0.0560 0.1112 0.8328 107 K 0.1383 0.1253 0.7364 108 H 0.3718 0.0595 0.5687 109 L 0.6731 0.0128 0.3140 110 K 0.7760 0.0072 0.2168 111 L 0.7982 0.0048 0.1970 112 A 0.7900 0.0081 0.2019 113 M 0.7629 0.0063 0.2307 114 T 0.6779 0.0140 0.3082 115 I 0.5564 0.0322 0.4114 116 A 0.3610 0.0706 0.5684 117 A 0.2413 0.0489 0.7097 118 P 0.1197 0.1522 0.7280 119 G 0.0655 0.1195 0.8150 120 E 0.2318 0.0308 0.7374 121 P 0.3041 0.0287 0.6672 122 P 0.3246 0.0591 0.6163 123 L 0.3045 0.0839 0.6116 124 N 0.2955 0.1205 0.5840 125 D 0.3517 0.0975 0.5508 126 L 0.4735 0.0606 0.4659 127 F 0.6166 0.0362 0.3472 128 V 0.6652 0.0324 0.3024 129 Q 0.4475 0.0650 0.4875 130 L 0.1494 0.4308 0.4198 131 N 0.0703 0.4826 0.4471 132 G 0.0597 0.5183 0.4221 133 F 0.0226 0.8134 0.1640 134 S 0.0098 0.8871 0.1031 135 N 0.0088 0.9032 0.0881 136 A 0.0085 0.9130 0.0785 137 L 0.0086 0.9048 0.0865 138 N 0.0088 0.8853 0.1059 139 R 0.0101 0.8592 0.1307 140 L 0.0118 0.8690 0.1192 141 I 0.0104 0.8718 0.1178 142 A 0.0130 0.8579 0.1292 143 L 0.0268 0.7408 0.2324 144 Q 0.0600 0.5330 0.4070 145 K 0.0712 0.3977 0.5311