# This file is the result of combining several RDB files, specifically # T0482.t06.str2.rdb (weight 1.54425) # T0482.t06.str4.rdb (weight 0.924988) # T0482.t06.pb.rdb (weight 0.789901) # T0482.t06.bys.rdb (weight 0.748322) # T0482.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 T0482.t06.str2.rdb # ============================================ # TARGET T0482 # 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 T0482.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 5.74721 # # ============================================ # Comments from T0482.t06.str4.rdb # ============================================ # TARGET T0482 # 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 T0482.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 5.74721 # # ============================================ # Comments from T0482.t06.pb.rdb # ============================================ # TARGET T0482 # 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 T0482.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 5.74721 # # ============================================ # Comments from T0482.t06.bys.rdb # ============================================ # TARGET T0482 # 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 T0482.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 5.74721 # # ============================================ # Comments from T0482.t06.alpha.rdb # ============================================ # TARGET T0482 # 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 T0482.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 5.74721 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.2855 0.1402 0.5743 2 F 0.3203 0.0817 0.5980 3 E 0.3051 0.0541 0.6408 4 P 0.2380 0.1323 0.6297 5 G 0.2399 0.1322 0.6279 6 H 0.4123 0.1123 0.4753 7 L 0.5026 0.1145 0.3829 8 H 0.5109 0.1217 0.3674 9 L 0.4914 0.1472 0.3613 10 V 0.4483 0.1362 0.4155 11 S 0.3876 0.0910 0.5214 12 L 0.2752 0.0569 0.6679 13 P 0.1545 0.1807 0.6648 14 G 0.1294 0.2240 0.6467 15 L 0.1972 0.1594 0.6434 16 D 0.1828 0.1090 0.7082 17 Q 0.1252 0.2651 0.6097 18 Q 0.1196 0.2923 0.5881 19 D 0.2143 0.1468 0.6388 20 I 0.4251 0.0561 0.5188 21 N 0.5678 0.0325 0.3996 22 I 0.7296 0.0160 0.2545 23 H 0.7483 0.0122 0.2395 24 I 0.7876 0.0096 0.2027 25 R 0.7665 0.0159 0.2176 26 Y 0.7812 0.0132 0.2056 27 E 0.7308 0.0261 0.2431 28 V 0.6849 0.0490 0.2661 29 R 0.5391 0.1062 0.3546 30 Q 0.4868 0.0924 0.4207 31 N 0.2755 0.0822 0.6422 32 A 0.0703 0.3955 0.5341 33 E 0.0543 0.3914 0.5543 34 S 0.0892 0.1863 0.7245 35 G 0.1262 0.0811 0.7927 36 A 0.4242 0.0540 0.5218 37 Y 0.7161 0.0185 0.2654 38 V 0.7633 0.0154 0.2213 39 H 0.7986 0.0080 0.1935 40 F 0.7806 0.0101 0.2092 41 D 0.7277 0.0152 0.2571 42 M 0.6625 0.0499 0.2876 43 D 0.5527 0.0608 0.3865 44 G 0.5702 0.0456 0.3842 45 E 0.6170 0.0508 0.3322 46 I 0.5574 0.0659 0.3767 47 D 0.2257 0.0951 0.6792 48 G 0.1277 0.0672 0.8051 49 K 0.4015 0.0159 0.5826 50 P 0.4776 0.0192 0.5032 51 F 0.3852 0.1102 0.5046 52 S 0.3032 0.1664 0.5304 53 D 0.2941 0.2280 0.4778 54 S 0.3297 0.1995 0.4707 55 F 0.4608 0.0883 0.4509 56 E 0.4458 0.0584 0.4959 57 L 0.3330 0.0290 0.6380 58 P 0.2084 0.0968 0.6948 59 R 0.0533 0.5261 0.4205 60 D 0.0409 0.6710 0.2882 61 T 0.0535 0.7248 0.2217 62 A 0.0649 0.7579 0.1772 63 F 0.0502 0.8012 0.1485 64 N 0.0361 0.8094 0.1546 65 F 0.0234 0.8313 0.1453 66 A 0.0127 0.8745 0.1128 67 S 0.0093 0.9020 0.0887 68 D 0.0094 0.9019 0.0886 69 A 0.0091 0.9065 0.0844 70 T 0.0087 0.9132 0.0781 71 R 0.0085 0.9210 0.0704 72 V 0.0089 0.9190 0.0721 73 A 0.0097 0.9103 0.0800 74 Q 0.0116 0.8871 0.1012 75 K 0.0190 0.7499 0.2311 76 H 0.0566 0.2878 0.6556 77 G 0.0512 0.1067 0.8420 78 L 0.1598 0.0661 0.7741 79 H 0.2018 0.0350 0.7631 80 P 0.0957 0.3088 0.5955 81 K 0.0940 0.3334 0.5726 82 F 0.1357 0.2903 0.5740 83 G 0.1583 0.2802 0.5615 84 A 0.2175 0.3578 0.4247 85 I 0.2265 0.4382 0.3353 86 T 0.1646 0.5561 0.2792 87 R 0.1361 0.5757 0.2882 88 V 0.0960 0.6098 0.2942 89 H 0.0796 0.6738 0.2466 90 K 0.0267 0.7906 0.1827 91 E 0.0263 0.8074 0.1663 92 Y 0.0292 0.8277 0.1431 93 D 0.0187 0.8550 0.1262 94 A 0.0149 0.8532 0.1319 95 M 0.0146 0.8543 0.1310 96 F 0.0113 0.8926 0.0961 97 E 0.0087 0.9072 0.0842 98 D 0.0089 0.9123 0.0787 99 I 0.0090 0.9076 0.0834 100 R 0.0093 0.9043 0.0864 101 A 0.0141 0.8630 0.1230 102 K 0.0419 0.7087 0.2493 103 L 0.1369 0.3966 0.4665 104 H 0.1764 0.2013 0.6222 105 A 0.2717 0.0874 0.6409 106 H 0.2289 0.0468 0.7243 107 P 0.1110 0.1787 0.7103 108 G 0.0449 0.1147 0.8405 109 E 0.2431 0.0296 0.7273 110 P 0.4106 0.0369 0.5524 111 V 0.4983 0.0306 0.4711 112 D 0.2823 0.0152 0.7026 113 L 0.0362 0.6528 0.3110 114 E 0.0235 0.7564 0.2201 115 R 0.0517 0.7531 0.1952 116 I 0.1131 0.6534 0.2335 117 I 0.1213 0.6015 0.2771 118 R 0.1468 0.4247 0.4285 119 H 0.1372 0.2599 0.6030 120 E 0.1254 0.2122 0.6623