# This file is the result of combining several RDB files, specifically # TR432.t06.str2.rdb (weight 1.54425) # TR432.t06.str4.rdb (weight 0.924988) # TR432.t06.pb.rdb (weight 0.789901) # TR432.t06.bys.rdb (weight 0.748322) # TR432.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 TR432.t06.str2.rdb # ============================================ # TARGET TR432 # 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 TR432.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 1424 # # ============================================ # Comments from TR432.t06.str4.rdb # ============================================ # TARGET TR432 # 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 TR432.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 1424 # # ============================================ # Comments from TR432.t06.pb.rdb # ============================================ # TARGET TR432 # 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 TR432.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 1424 # # ============================================ # Comments from TR432.t06.bys.rdb # ============================================ # TARGET TR432 # 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 TR432.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 1424 # # ============================================ # Comments from TR432.t06.alpha.rdb # ============================================ # TARGET TR432 # 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 TR432.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 1424 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 S 0.1830 0.1199 0.6972 2 M 0.1524 0.1590 0.6886 3 Q 0.1572 0.1794 0.6635 4 E 0.1114 0.3065 0.5821 5 E 0.1198 0.3252 0.5551 6 D 0.1180 0.3122 0.5698 7 T 0.1104 0.3617 0.5279 8 F 0.0498 0.6950 0.2552 9 R 0.0160 0.8619 0.1221 10 E 0.0098 0.9073 0.0828 11 L 0.0086 0.9165 0.0749 12 R 0.0083 0.9210 0.0706 13 I 0.0083 0.9233 0.0685 14 F 0.0083 0.9233 0.0684 15 L 0.0083 0.9217 0.0700 16 R 0.0083 0.9215 0.0701 17 N 0.0083 0.9228 0.0689 18 V 0.0084 0.9201 0.0714 19 T 0.0084 0.9170 0.0745 20 H 0.0085 0.9178 0.0737 21 R 0.0091 0.9098 0.0811 22 L 0.0174 0.8667 0.1159 23 A 0.0218 0.8010 0.1772 24 I 0.0483 0.6192 0.3324 25 D 0.0953 0.3637 0.5410 26 K 0.0351 0.4738 0.4912 27 R 0.0610 0.4036 0.5355 28 F 0.1723 0.2459 0.5818 29 R 0.2453 0.2035 0.5512 30 V 0.2678 0.2751 0.4571 31 F 0.2757 0.2057 0.5187 32 T 0.3148 0.1405 0.5447 33 K 0.3458 0.0376 0.6166 34 P 0.2995 0.0543 0.6463 35 V 0.3475 0.0443 0.6082 36 D 0.1993 0.0159 0.7848 37 P 0.0189 0.6682 0.3129 38 D 0.0236 0.5569 0.4195 39 E 0.0582 0.4828 0.4590 40 V 0.2099 0.1195 0.6707 41 P 0.1219 0.3031 0.5750 42 D 0.1164 0.3293 0.5543 43 Y 0.1807 0.4766 0.3426 44 V 0.2689 0.4194 0.3117 45 T 0.3820 0.3390 0.2790 46 V 0.4078 0.2799 0.3123 47 I 0.3884 0.2282 0.3834 48 K 0.3326 0.1439 0.5234 49 Q 0.2477 0.0650 0.6873 50 P 0.1702 0.1533 0.6765 51 M 0.1827 0.2014 0.6159 52 D 0.1814 0.1649 0.6536 53 L 0.0222 0.7062 0.2716 54 S 0.0140 0.8399 0.1460 55 S 0.0180 0.8974 0.0845 56 V 0.0137 0.9110 0.0753 57 I 0.0119 0.9088 0.0793 58 S 0.0126 0.8923 0.0951 59 K 0.0196 0.8400 0.1404 60 I 0.0448 0.7596 0.1956 61 D 0.0427 0.6402 0.3171 62 L 0.0438 0.3620 0.5942 63 H 0.0634 0.2100 0.7265 64 K 0.1938 0.1900 0.6162 65 Y 0.3064 0.1336 0.5600 66 L 0.2757 0.0916 0.6327 67 T 0.2244 0.0431 0.7325 68 V 0.0183 0.7287 0.2529 69 K 0.0101 0.8596 0.1303 70 D 0.0109 0.9046 0.0844 71 Y 0.0120 0.9056 0.0825 72 L 0.0101 0.9107 0.0792 73 R 0.0091 0.9078 0.0831 74 D 0.0099 0.9055 0.0846 75 I 0.0090 0.9163 0.0747 76 D 0.0085 0.9194 0.0721 77 L 0.0092 0.9171 0.0737 78 I 0.0114 0.9080 0.0806 79 C 0.0138 0.8929 0.0932 80 S 0.0134 0.8740 0.1126 81 N 0.0210 0.7846 0.1944 82 A 0.0311 0.8073 0.1615 83 L 0.0247 0.8344 0.1409 84 E 0.0523 0.7037 0.2440 85 Y 0.1085 0.4668 0.4247 86 N 0.1861 0.1359 0.6780 87 P 0.0639 0.3677 0.5684 88 D 0.0722 0.2867 0.6411 89 R 0.0724 0.2010 0.7266 90 D 0.1647 0.0927 0.7425 91 P 0.0576 0.3878 0.5546 92 G 0.0618 0.3220 0.6161 93 D 0.1116 0.3864 0.5020 94 R 0.1658 0.5063 0.3279 95 L 0.2209 0.5456 0.2335 96 I 0.1082 0.7354 0.1564 97 R 0.0377 0.8542 0.1080 98 H 0.0145 0.9004 0.0852 99 R 0.0110 0.9048 0.0842 100 A 0.0086 0.9173 0.0742 101 C 0.0083 0.9213 0.0703 102 A 0.0083 0.9228 0.0689 103 L 0.0083 0.9210 0.0706 104 R 0.0084 0.9197 0.0719 105 D 0.0083 0.9214 0.0703 106 T 0.0083 0.9215 0.0701 107 A 0.0084 0.9202 0.0715 108 Y 0.0084 0.9187 0.0730 109 A 0.0084 0.9194 0.0722 110 I 0.0087 0.9132 0.0782 111 I 0.0101 0.8936 0.0963 112 K 0.0105 0.8648 0.1247 113 E 0.0177 0.7683 0.2140 114 E 0.0537 0.5740 0.3723 115 L 0.0830 0.4058 0.5112 116 D 0.0803 0.3616 0.5581 117 E 0.0554 0.5041 0.4405 118 D 0.0656 0.4997 0.4346 119 F 0.0688 0.6173 0.3139 120 E 0.0657 0.6754 0.2589 121 Q 0.0743 0.6540 0.2716 122 L 0.0896 0.6020 0.3084 123 C 0.0991 0.6022 0.2986 124 E 0.0590 0.6818 0.2592 125 E 0.0777 0.6509 0.2715 126 I 0.1002 0.5598 0.3400 127 Q 0.1163 0.4694 0.4143 128 E 0.1304 0.3583 0.5114 129 S 0.1363 0.2216 0.6420 130 R 0.1630 0.1359 0.7011