# This file is the result of combining several RDB files, specifically # T0462.t04.str2.rdb (weight 1.54425) # T0462.t04.str4.rdb (weight 0.924988) # T0462.t04.pb.rdb (weight 0.789901) # T0462.t04.bys.rdb (weight 0.748322) # T0462.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 T0462.t04.str2.rdb # ============================================ # TARGET T0462 # 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 T0462.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 71.4163 # # ============================================ # Comments from T0462.t04.str4.rdb # ============================================ # TARGET T0462 # 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 T0462.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 71.4163 # # ============================================ # Comments from T0462.t04.pb.rdb # ============================================ # TARGET T0462 # 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 T0462.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 71.4163 # # ============================================ # Comments from T0462.t04.bys.rdb # ============================================ # TARGET T0462 # 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 T0462.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 71.4163 # # ============================================ # Comments from T0462.t04.alpha.rdb # ============================================ # TARGET T0462 # 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 T0462.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 71.4163 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.3627 0.0258 0.6115 2 K 0.2849 0.0210 0.6942 3 L 0.1868 0.3586 0.4546 4 S 0.1332 0.4628 0.4039 5 R 0.1997 0.2888 0.5116 6 L 0.3064 0.0636 0.6300 7 V 0.2532 0.0377 0.7091 8 P 0.1364 0.1187 0.7449 9 G 0.0723 0.0915 0.8362 10 V 0.3293 0.0239 0.6468 11 P 0.5967 0.0205 0.3828 12 A 0.7442 0.0093 0.2465 13 R 0.7788 0.0078 0.2134 14 I 0.7058 0.0049 0.2893 15 K 0.6854 0.0154 0.2992 16 R 0.7623 0.0071 0.2306 17 L 0.6666 0.0176 0.3158 18 E 0.5034 0.0375 0.4591 19 V 0.2934 0.1047 0.6019 20 S 0.1411 0.1895 0.6694 21 G 0.0488 0.4748 0.4765 22 E 0.0341 0.7299 0.2360 23 L 0.0210 0.8517 0.1272 24 H 0.0121 0.8951 0.0929 25 E 0.0097 0.9147 0.0756 26 K 0.0100 0.9113 0.0787 27 L 0.0122 0.8910 0.0967 28 V 0.0157 0.8563 0.1280 29 G 0.0250 0.6993 0.2757 30 M 0.0825 0.3235 0.5939 31 G 0.1141 0.1275 0.7585 32 F 0.2463 0.0645 0.6892 33 V 0.3072 0.0292 0.6635 34 P 0.1493 0.1309 0.7199 35 G 0.0641 0.1096 0.8263 36 E 0.3638 0.0284 0.6079 37 E 0.6601 0.0145 0.3253 38 I 0.7729 0.0081 0.2189 39 E 0.7805 0.0082 0.2113 40 I 0.7544 0.0056 0.2400 41 V 0.7462 0.0220 0.2318 42 Q 0.7456 0.0214 0.2330 43 V 0.6734 0.0377 0.2889 44 A 0.4747 0.0281 0.4972 45 P 0.2990 0.0878 0.6132 46 L 0.1567 0.1299 0.7134 47 G 0.1124 0.0815 0.8061 48 D 0.2397 0.0237 0.7366 49 P 0.4300 0.0630 0.5069 50 I 0.7148 0.0370 0.2481 51 V 0.7968 0.0074 0.1958 52 C 0.8016 0.0069 0.1915 53 K 0.7529 0.0063 0.2408 54 I 0.6599 0.0320 0.3081 55 G 0.3733 0.0595 0.5672 56 N 0.2003 0.0849 0.7148 57 R 0.4704 0.0623 0.4673 58 N 0.6402 0.0534 0.3064 59 I 0.7054 0.0726 0.2221 60 T 0.6831 0.0844 0.2324 61 L 0.6274 0.1179 0.2547 62 R 0.3425 0.2137 0.4439 63 K 0.1207 0.5411 0.3382 64 R 0.0717 0.6388 0.2895 65 E 0.0833 0.5846 0.3321 66 A 0.2445 0.3365 0.4190 67 D 0.2169 0.2611 0.5220 68 L 0.5460 0.0633 0.3907 69 I 0.6349 0.0178 0.3472 70 E 0.7358 0.0118 0.2524 71 V 0.7597 0.0095 0.2308 72 E 0.7134 0.0165 0.2701 73 V 0.6330 0.0203 0.3467 74 V 0.3871 0.0718 0.5412 75 G 0.2159 0.0906 0.6934 76 G 0.1617 0.1238 0.7145 77 E 0.2459 0.1106 0.6434 78 L 0.3482 0.0582 0.5936 79 P 0.3383 0.1075 0.5542 80 L 0.4400 0.1510 0.4089 81 I 0.5288 0.1158 0.3554 82 L 0.5176 0.1064 0.3760 83 A 0.4004 0.1186 0.4810 84 D 0.2704 0.1513 0.5783 85 D 0.1346 0.1289 0.7365 86 G 0.1163 0.0960 0.7877 87 T 0.3408 0.0692 0.5900 88 Y 0.5403 0.0467 0.4130 89 E 0.6178 0.0521 0.3301 90 I 0.6452 0.0451 0.3097 91 T 0.5781 0.0816 0.3403 92 K 0.5145 0.1110 0.3745 93 L 0.3611 0.1846 0.4543 94 N 0.1923 0.1765 0.6311 95 G 0.1161 0.1450 0.7390 96 G 0.1528 0.1631 0.6840 97 R 0.2002 0.3093 0.4904 98 R 0.2150 0.4571 0.3279 99 F 0.1744 0.5929 0.2326 100 L 0.1353 0.7055 0.1592 101 F 0.0992 0.7784 0.1224 102 R 0.1059 0.7618 0.1324 103 M 0.1153 0.7072 0.1775 104 K 0.0986 0.6617 0.2397 105 N 0.1361 0.4866 0.3773 106 L 0.2803 0.2474 0.4723 107 G 0.3383 0.1743 0.4874 108 I 0.3680 0.1468 0.4852 109 E 0.3248 0.1731 0.5021 110 S 0.1382 0.1209 0.7409 111 G 0.0932 0.0804 0.8264 112 K 0.4168 0.0169 0.5663 113 K 0.6979 0.0084 0.2938 114 I 0.7771 0.0080 0.2148 115 Q 0.7839 0.0063 0.2098 116 V 0.7510 0.0077 0.2414 117 S 0.5517 0.0354 0.4129 118 G 0.3060 0.0441 0.6499 119 R 0.2762 0.0497 0.6741 120 R 0.2471 0.1800 0.5729 121 Y 0.2898 0.1472 0.5629 122 Y 0.3795 0.0974 0.5231 123 I 0.3932 0.1014 0.5054 124 E 0.3522 0.1206 0.5271 125 G 0.3040 0.1463 0.5497 126 R 0.3848 0.2195 0.3957 127 E 0.4850 0.2442 0.2708 128 I 0.5280 0.2290 0.2430 129 D 0.4260 0.2504 0.3236 130 L 0.2916 0.3670 0.3415 131 G 0.2245 0.3130 0.4625 132 Y 0.2086 0.2221 0.5693 133 G 0.1852 0.1924 0.6224 134 E 0.2174 0.2757 0.5068 135 A 0.3091 0.1885 0.5024 136 T 0.4044 0.1015 0.4942 137 K 0.6409 0.0314 0.3277 138 I 0.7204 0.0140 0.2656 139 W 0.7072 0.0167 0.2761 140 V 0.6015 0.0258 0.3727 141 R 0.4318 0.0754 0.4928 142 R 0.3458 0.0692 0.5850 143 V 0.3874 0.0415 0.5711 144 S 0.3574 0.0521 0.5905 145 D 0.2346 0.2889 0.4766 146 A 0.1792 0.2985 0.5223 147 G 0.1646 0.3282 0.5072 148 E 0.1637 0.3856 0.4507 149 E 0.1893 0.2788 0.5320 150 S 0.1842 0.1579 0.6579 151 H 0.2522 0.0713 0.6764 152 P 0.2340 0.1483 0.6177 153 Q 0.2029 0.1808 0.6163 154 K 0.1965 0.1597 0.6438