# This file is the result of combining several RDB files, specifically # T0401.t06.str2.rdb (weight 1.54425) # T0401.t06.str4.rdb (weight 0.924988) # T0401.t06.pb.rdb (weight 0.789901) # T0401.t06.bys.rdb (weight 0.748322) # T0401.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 T0401.t06.str2.rdb # ============================================ # TARGET T0401 # 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 T0401.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 218 # # ============================================ # Comments from T0401.t06.str4.rdb # ============================================ # TARGET T0401 # 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 T0401.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 218 # # ============================================ # Comments from T0401.t06.pb.rdb # ============================================ # TARGET T0401 # 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 T0401.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 218 # # ============================================ # Comments from T0401.t06.bys.rdb # ============================================ # TARGET T0401 # 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 T0401.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 218 # # ============================================ # Comments from T0401.t06.alpha.rdb # ============================================ # TARGET T0401 # 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 T0401.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 218 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.3201 0.1104 0.5695 2 E 0.3412 0.1423 0.5165 3 V 0.4366 0.1825 0.3809 4 I 0.3982 0.2283 0.3735 5 E 0.3441 0.2387 0.4172 6 S 0.2628 0.2934 0.4438 7 K 0.1662 0.3884 0.4454 8 W 0.1814 0.3629 0.4557 9 Y 0.1889 0.3051 0.5060 10 K 0.1441 0.2711 0.5848 11 K 0.1261 0.2295 0.6445 12 D 0.1005 0.1526 0.7469 13 G 0.0789 0.1333 0.7878 14 A 0.1712 0.0843 0.7445 15 S 0.1788 0.0315 0.7898 16 S 0.0156 0.7088 0.2757 17 A 0.0122 0.8168 0.1710 18 S 0.0168 0.8398 0.1434 19 I 0.0104 0.8953 0.0943 20 D 0.0084 0.9148 0.0768 21 D 0.0084 0.9208 0.0708 22 V 0.0084 0.9216 0.0701 23 E 0.0084 0.9161 0.0754 24 K 0.0084 0.9150 0.0765 25 L 0.0117 0.8102 0.1781 26 L 0.0598 0.3725 0.5678 27 N 0.0391 0.1274 0.8335 28 T 0.1768 0.0596 0.7636 29 T 0.2041 0.0727 0.7232 30 L 0.2085 0.0383 0.7531 31 P 0.1295 0.3354 0.5352 32 K 0.0141 0.7496 0.2363 33 Q 0.0111 0.8442 0.1446 34 Y 0.0125 0.8918 0.0957 35 K 0.0091 0.9160 0.0748 36 S 0.0090 0.9161 0.0749 37 F 0.0107 0.9078 0.0816 38 L 0.0235 0.8748 0.1018 39 L 0.0269 0.8535 0.1196 40 W 0.0552 0.7009 0.2439 41 S 0.0912 0.4184 0.4904 42 N 0.0883 0.1655 0.7462 43 G 0.0944 0.0937 0.8119 44 G 0.2200 0.0875 0.6925 45 E 0.3482 0.0901 0.5617 46 G 0.4029 0.0811 0.5159 47 K 0.4336 0.0742 0.4922 48 L 0.2988 0.0883 0.6129 49 G 0.1824 0.0847 0.7329 50 D 0.1937 0.1302 0.6762 51 N 0.2698 0.1242 0.6060 52 Y 0.4615 0.1138 0.4248 53 I 0.6103 0.0627 0.3270 54 Y 0.6601 0.0581 0.2818 55 I 0.5703 0.0809 0.3488 56 W 0.4928 0.0784 0.4288 57 A 0.3192 0.0677 0.6131 58 I 0.0564 0.6169 0.3267 59 E 0.0237 0.7713 0.2050 60 D 0.0319 0.8064 0.1617 61 V 0.0381 0.8159 0.1461 62 I 0.0325 0.8232 0.1443 63 A 0.0435 0.7697 0.1868 64 Y 0.0611 0.6687 0.2702 65 N 0.0815 0.5153 0.4032 66 H 0.0508 0.6115 0.3377 67 D 0.0628 0.5626 0.3745 68 Y 0.1081 0.4561 0.4358 69 G 0.1326 0.3997 0.4677 70 I 0.1536 0.4504 0.3960 71 Q 0.1017 0.5522 0.3461 72 K 0.0746 0.5940 0.3314 73 Y 0.1134 0.4172 0.4694 74 L 0.2027 0.1982 0.5991 75 Q 0.1682 0.1920 0.6397 76 K 0.0829 0.4341 0.4830 77 E 0.1284 0.2470 0.6246 78 Y 0.4779 0.0595 0.4626 79 W 0.6861 0.0213 0.2926 80 A 0.7507 0.0145 0.2348 81 F 0.7371 0.0203 0.2425 82 G 0.5643 0.0321 0.4036 83 M 0.3700 0.0996 0.5303 84 D 0.2504 0.0858 0.6638 85 G 0.1540 0.0879 0.7581 86 D 0.1867 0.0923 0.7210 87 I 0.3601 0.0606 0.5793 88 G 0.6818 0.0285 0.2898 89 Y 0.7752 0.0103 0.2146 90 I 0.8118 0.0061 0.1822 91 L 0.8011 0.0088 0.1901 92 H 0.7228 0.0094 0.2678 93 L 0.5453 0.0846 0.3701 94 S 0.2840 0.1357 0.5803 95 D 0.1417 0.1387 0.7196 96 N 0.1093 0.1161 0.7746 97 S 0.2888 0.0632 0.6480 98 I 0.5133 0.0298 0.4569 99 Y 0.6624 0.0227 0.3150 100 R 0.7594 0.0085 0.2320 101 V 0.7791 0.0085 0.2124 102 D 0.7167 0.0111 0.2722 103 L 0.6485 0.0332 0.3183 104 G 0.3734 0.0663 0.5603 105 D 0.2831 0.0695 0.6474 106 L 0.2092 0.1443 0.6465 107 D 0.2138 0.1130 0.6732 108 I 0.0994 0.3802 0.5204 109 T 0.0985 0.4128 0.4887 110 S 0.1799 0.3658 0.4543 111 I 0.3183 0.2969 0.3848 112 K 0.3237 0.3527 0.3236 113 Y 0.3885 0.2590 0.3524 114 I 0.2926 0.2687 0.4388 115 A 0.2200 0.1808 0.5992 116 P 0.0642 0.4280 0.5077 117 S 0.0955 0.3916 0.5129 118 F 0.0192 0.7413 0.2395 119 D 0.0095 0.8604 0.1301 120 D 0.0085 0.9084 0.0831 121 F 0.0093 0.9079 0.0827 122 L 0.0096 0.9001 0.0903 123 G 0.0093 0.8862 0.1045 124 K 0.0130 0.8373 0.1497 125 A 0.0376 0.7435 0.2190 126 I 0.0709 0.6669 0.2622 127 Y 0.1180 0.5491 0.3329 128 L 0.1139 0.4555 0.4306 129 N 0.1211 0.3491 0.5297 130 F 0.1060 0.4683 0.4258 131 N 0.1267 0.4498 0.4234 132 K 0.1075 0.5455 0.3471 133 L 0.0888 0.6190 0.2922 134 Q 0.0913 0.6116 0.2971 135 N 0.1154 0.5184 0.3662 136 V 0.1348 0.4724 0.3928 137 A 0.0857 0.4505 0.4638 138 N 0.0881 0.2978 0.6141 139 N 0.1027 0.2170 0.6802 140 N 0.1458 0.1599 0.6943 141 L 0.2864 0.0971 0.6165 142 T 0.3531 0.0801 0.5668 143 T 0.3461 0.0797 0.5743