# This file is the result of combining several RDB files, specifically # T0401.t04.str2.rdb (weight 1.54425) # T0401.t04.str4.rdb (weight 0.924988) # T0401.t04.pb.rdb (weight 0.789901) # T0401.t04.bys.rdb (weight 0.748322) # T0401.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 T0401.t04.str2.rdb # ============================================ # TARGET T0401 # 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 T0401.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 180 # # ============================================ # Comments from T0401.t04.str4.rdb # ============================================ # TARGET T0401 # 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 T0401.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 180 # # ============================================ # Comments from T0401.t04.pb.rdb # ============================================ # TARGET T0401 # 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 T0401.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 180 # # ============================================ # Comments from T0401.t04.bys.rdb # ============================================ # TARGET T0401 # 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 T0401.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 180 # # ============================================ # Comments from T0401.t04.alpha.rdb # ============================================ # TARGET T0401 # 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 T0401.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 180 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.2894 0.1053 0.6052 2 E 0.3235 0.1314 0.5451 3 V 0.4164 0.1815 0.4021 4 I 0.3750 0.2030 0.4220 5 E 0.2885 0.2119 0.4996 6 S 0.2139 0.3054 0.4807 7 K 0.1581 0.3798 0.4621 8 W 0.1976 0.3417 0.4606 9 Y 0.2196 0.2640 0.5164 10 K 0.1846 0.2812 0.5342 11 K 0.1390 0.2806 0.5804 12 D 0.1162 0.1784 0.7054 13 G 0.0956 0.1297 0.7748 14 A 0.1557 0.1168 0.7276 15 S 0.1653 0.0589 0.7758 16 S 0.0154 0.7031 0.2815 17 A 0.0102 0.8426 0.1472 18 S 0.0134 0.8834 0.1032 19 I 0.0088 0.9138 0.0774 20 D 0.0085 0.9162 0.0753 21 D 0.0084 0.9221 0.0695 22 V 0.0085 0.9193 0.0722 23 E 0.0085 0.9211 0.0704 24 K 0.0089 0.9101 0.0810 25 L 0.0160 0.8007 0.1833 26 L 0.0608 0.4052 0.5340 27 N 0.0436 0.1503 0.8062 28 T 0.1838 0.0618 0.7544 29 T 0.2032 0.0699 0.7269 30 L 0.2005 0.0428 0.7566 31 P 0.1235 0.2579 0.6186 32 K 0.0131 0.7455 0.2415 33 Q 0.0141 0.8301 0.1559 34 Y 0.0101 0.9056 0.0842 35 K 0.0094 0.9164 0.0742 36 S 0.0090 0.9179 0.0731 37 F 0.0101 0.9144 0.0755 38 L 0.0143 0.8977 0.0879 39 L 0.0195 0.8707 0.1098 40 W 0.0546 0.7319 0.2135 41 S 0.1132 0.4076 0.4791 42 N 0.1092 0.1702 0.7206 43 G 0.1203 0.1127 0.7670 44 G 0.2354 0.0972 0.6674 45 E 0.3905 0.0852 0.5242 46 G 0.4448 0.0600 0.4952 47 K 0.4794 0.0629 0.4577 48 L 0.3669 0.0805 0.5526 49 G 0.1907 0.0895 0.7198 50 D 0.1366 0.1569 0.7065 51 N 0.1791 0.1161 0.7048 52 Y 0.4628 0.0553 0.4819 53 I 0.6649 0.0343 0.3009 54 Y 0.7267 0.0270 0.2463 55 I 0.6761 0.0447 0.2792 56 W 0.5480 0.0689 0.3831 57 A 0.3397 0.0878 0.5725 58 I 0.0824 0.5564 0.3612 59 E 0.0462 0.6701 0.2836 60 D 0.0503 0.7246 0.2251 61 V 0.0368 0.7764 0.1869 62 I 0.0458 0.7812 0.1730 63 A 0.0573 0.7503 0.1923 64 Y 0.0838 0.6498 0.2664 65 N 0.0969 0.4995 0.4036 66 H 0.0395 0.6417 0.3188 67 D 0.0510 0.5750 0.3740 68 Y 0.1022 0.4378 0.4600 69 G 0.1180 0.3853 0.4968 70 I 0.1275 0.5175 0.3550 71 Q 0.0867 0.6078 0.3055 72 K 0.0560 0.6773 0.2667 73 Y 0.0780 0.5497 0.3723 74 L 0.1592 0.3568 0.4840 75 Q 0.1547 0.2756 0.5697 76 K 0.0976 0.4209 0.4815 77 E 0.1474 0.1990 0.6536 78 Y 0.4595 0.0413 0.4992 79 W 0.6640 0.0198 0.3162 80 A 0.7572 0.0115 0.2313 81 F 0.7208 0.0224 0.2567 82 G 0.6212 0.0291 0.3496 83 M 0.4313 0.0775 0.4912 84 D 0.2275 0.0901 0.6824 85 G 0.1473 0.0876 0.7651 86 D 0.1705 0.0983 0.7312 87 I 0.3852 0.0634 0.5514 88 G 0.6719 0.0257 0.3023 89 Y 0.7717 0.0091 0.2193 90 I 0.8116 0.0049 0.1835 91 L 0.8080 0.0062 0.1858 92 H 0.7245 0.0081 0.2674 93 L 0.6096 0.0878 0.3026 94 S 0.3621 0.1162 0.5217 95 D 0.1380 0.1264 0.7356 96 N 0.1122 0.1027 0.7851 97 S 0.2906 0.0510 0.6584 98 I 0.5205 0.0298 0.4497 99 Y 0.6271 0.0289 0.3440 100 R 0.7435 0.0111 0.2454 101 V 0.7291 0.0119 0.2590 102 D 0.6427 0.0171 0.3402 103 L 0.5078 0.0818 0.4105 104 G 0.3235 0.1085 0.5681 105 D 0.2882 0.0933 0.6185 106 L 0.2562 0.1369 0.6070 107 D 0.2403 0.1002 0.6595 108 I 0.0896 0.4000 0.5104 109 T 0.0782 0.3499 0.5719 110 S 0.1644 0.3029 0.5326 111 I 0.3480 0.1640 0.4881 112 K 0.4401 0.1761 0.3837 113 Y 0.4705 0.1770 0.3526 114 I 0.3681 0.1673 0.4646 115 A 0.2384 0.1449 0.6167 116 P 0.1271 0.3244 0.5485 117 S 0.1394 0.2680 0.5925 118 F 0.0197 0.6789 0.3014 119 D 0.0103 0.8334 0.1563 120 D 0.0085 0.9088 0.0827 121 F 0.0087 0.9079 0.0833 122 L 0.0090 0.8978 0.0932 123 G 0.0096 0.8759 0.1145 124 K 0.0127 0.8557 0.1315 125 A 0.0297 0.8161 0.1543 126 I 0.0465 0.7779 0.1757 127 Y 0.0766 0.6976 0.2258 128 L 0.0989 0.5778 0.3234 129 N 0.1172 0.4160 0.4668 130 F 0.1023 0.4638 0.4339 131 N 0.1084 0.4141 0.4775 132 K 0.1206 0.4601 0.4194 133 L 0.1264 0.5146 0.3590 134 Q 0.1540 0.5151 0.3308 135 N 0.2051 0.4412 0.3537 136 V 0.1710 0.4468 0.3822 137 A 0.1360 0.3947 0.4693 138 N 0.1115 0.3159 0.5726 139 N 0.0952 0.2488 0.6560 140 N 0.1374 0.1779 0.6847 141 L 0.2866 0.1145 0.5989 142 T 0.3214 0.1025 0.5761 143 T 0.3393 0.0854 0.5753