# This file is the result of combining several RDB files, specifically # T0451.t06.str2.rdb (weight 1.54425) # T0451.t06.str4.rdb (weight 0.924988) # T0451.t06.pb.rdb (weight 0.789901) # T0451.t06.bys.rdb (weight 0.748322) # T0451.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 T0451.t06.str2.rdb # ============================================ # TARGET T0451 # 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 T0451.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 436 # # ============================================ # Comments from T0451.t06.str4.rdb # ============================================ # TARGET T0451 # 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 T0451.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 436 # # ============================================ # Comments from T0451.t06.pb.rdb # ============================================ # TARGET T0451 # 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 T0451.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 436 # # ============================================ # Comments from T0451.t06.bys.rdb # ============================================ # TARGET T0451 # 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 T0451.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 436 # # ============================================ # Comments from T0451.t06.alpha.rdb # ============================================ # TARGET T0451 # 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 T0451.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 436 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.3065 0.1658 0.5277 2 M 0.3023 0.1385 0.5592 3 T 0.2681 0.1352 0.5967 4 H 0.2182 0.1729 0.6089 5 Y 0.2009 0.1459 0.6532 6 S 0.1610 0.1611 0.6779 7 D 0.0571 0.4401 0.5028 8 N 0.0494 0.4889 0.4617 9 T 0.0745 0.5873 0.3382 10 L 0.0339 0.7741 0.1920 11 K 0.0193 0.8562 0.1246 12 V 0.0175 0.8741 0.1084 13 A 0.0109 0.9004 0.0887 14 H 0.0087 0.9148 0.0765 15 Q 0.0087 0.9179 0.0734 16 G 0.0084 0.9225 0.0691 17 F 0.0083 0.9203 0.0713 18 E 0.0083 0.9233 0.0684 19 F 0.0083 0.9223 0.0693 20 F 0.0084 0.9210 0.0706 21 T 0.0084 0.9165 0.0750 22 Q 0.0086 0.9091 0.0823 23 G 0.0106 0.8787 0.1108 24 L 0.0171 0.8478 0.1351 25 A 0.0235 0.6644 0.3121 26 T 0.0482 0.2816 0.6702 27 G 0.0401 0.1542 0.8057 28 E 0.0883 0.2508 0.6609 29 W 0.0198 0.7780 0.2022 30 Q 0.0099 0.8742 0.1159 31 K 0.0093 0.9072 0.0835 32 F 0.0094 0.9104 0.0802 33 L 0.0089 0.9015 0.0895 34 D 0.0115 0.8476 0.1409 35 M 0.0168 0.7654 0.2177 36 L 0.0548 0.4695 0.4757 37 T 0.0979 0.3315 0.5707 38 E 0.0591 0.3858 0.5551 39 D 0.1254 0.2322 0.6424 40 F 0.4185 0.0997 0.4818 41 T 0.6392 0.0465 0.3144 42 F 0.7167 0.0271 0.2562 43 W 0.6580 0.0350 0.3069 44 F 0.4888 0.0243 0.4869 45 P 0.2978 0.0835 0.6187 46 M 0.2138 0.1151 0.6711 47 G 0.2018 0.0895 0.7088 48 E 0.1629 0.1983 0.6388 49 F 0.1670 0.2224 0.6107 50 H 0.1333 0.1940 0.6727 51 G 0.1302 0.1583 0.7114 52 L 0.2153 0.1845 0.6001 53 N 0.2286 0.2150 0.5564 54 V 0.1877 0.2685 0.5438 55 G 0.1360 0.3073 0.5567 56 K 0.0168 0.7687 0.2144 57 E 0.0096 0.8777 0.1127 58 R 0.0088 0.9169 0.0743 59 A 0.0084 0.9197 0.0720 60 K 0.0084 0.9183 0.0733 61 E 0.0083 0.9196 0.0721 62 F 0.0086 0.9101 0.0813 63 F 0.0088 0.9047 0.0865 64 T 0.0091 0.8933 0.0975 65 Y 0.0113 0.8580 0.1307 66 V 0.0244 0.7980 0.1776 67 S 0.0202 0.7851 0.1946 68 E 0.0215 0.7101 0.2684 69 S 0.0464 0.5524 0.4012 70 F 0.1156 0.3423 0.5421 71 H 0.1091 0.3169 0.5740 72 T 0.1176 0.2328 0.6496 73 G 0.1610 0.1500 0.6891 74 I 0.3566 0.1149 0.5285 75 Q 0.5192 0.0802 0.4006 76 I 0.6089 0.0555 0.3356 77 S 0.6145 0.0391 0.3465 78 S 0.6193 0.0317 0.3490 79 L 0.5858 0.0684 0.3458 80 D 0.5460 0.0882 0.3657 81 R 0.6802 0.0455 0.2743 82 V 0.6490 0.0416 0.3094 83 T 0.6290 0.0424 0.3286 84 S 0.4911 0.0759 0.4330 85 N 0.2711 0.0658 0.6632 86 E 0.1587 0.1205 0.7208 87 T 0.3619 0.0565 0.5816 88 T 0.7120 0.0125 0.2755 89 V 0.7776 0.0071 0.2153 90 V 0.8214 0.0047 0.1738 91 F 0.8240 0.0047 0.1712 92 E 0.8171 0.0054 0.1775 93 F 0.7769 0.0090 0.2142 94 R 0.6864 0.0267 0.2869 95 D 0.5466 0.0916 0.3618 96 E 0.4757 0.1063 0.4180 97 G 0.4736 0.1084 0.4179 98 L 0.5063 0.1051 0.3887 99 F 0.4516 0.1137 0.4347 100 L 0.2500 0.1161 0.6339 101 G 0.1706 0.0703 0.7591 102 K 0.3922 0.0266 0.5812 103 P 0.5264 0.0405 0.4331 104 Y 0.5172 0.0843 0.3984 105 K 0.5306 0.0860 0.3833 106 N 0.5679 0.0580 0.3741 107 R 0.6208 0.0475 0.3317 108 V 0.7754 0.0142 0.2104 109 A 0.7984 0.0065 0.1951 110 V 0.8165 0.0057 0.1778 111 S 0.8279 0.0042 0.1679 112 F 0.8182 0.0052 0.1766 113 D 0.8040 0.0056 0.1905 114 V 0.7355 0.0119 0.2526 115 R 0.4931 0.0636 0.4433 116 G 0.1882 0.0556 0.7562 117 D 0.1380 0.0859 0.7761 118 K 0.5454 0.0207 0.4339 119 I 0.6550 0.0177 0.3274 120 C 0.6396 0.0315 0.3289 121 S 0.7579 0.0218 0.2202 122 Y 0.7120 0.0425 0.2455 123 R 0.7083 0.0669 0.2248 124 E 0.6456 0.1067 0.2477 125 Y 0.5210 0.1361 0.3429 126 F 0.4245 0.0877 0.4878 127 G 0.2176 0.0654 0.7170 128 S 0.1124 0.2949 0.5927 129 D 0.0913 0.2853 0.6234 130 G 0.1112 0.2050 0.6838 131 K 0.1360 0.1965 0.6675 132 S 0.1631 0.1789 0.6580 133 N 0.1587 0.1803 0.6611