# This file is the result of combining several RDB files, specifically # T0473.t06.str2.rdb (weight 1.54425) # T0473.t06.str4.rdb (weight 0.924988) # T0473.t06.pb.rdb (weight 0.789901) # T0473.t06.bys.rdb (weight 0.748322) # T0473.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 T0473.t06.str2.rdb # ============================================ # TARGET T0473 # 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 T0473.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 23.2886 # # ============================================ # Comments from T0473.t06.str4.rdb # ============================================ # TARGET T0473 # 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 T0473.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 23.2886 # # ============================================ # Comments from T0473.t06.pb.rdb # ============================================ # TARGET T0473 # 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 T0473.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 23.2886 # # ============================================ # Comments from T0473.t06.bys.rdb # ============================================ # TARGET T0473 # 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 T0473.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 23.2886 # # ============================================ # Comments from T0473.t06.alpha.rdb # ============================================ # TARGET T0473 # 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 T0473.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 23.2886 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.3394 0.0480 0.6126 2 K 0.3854 0.0381 0.5765 3 I 0.3660 0.0439 0.5901 4 T 0.2162 0.0521 0.7317 5 K 0.0633 0.4829 0.4539 6 D 0.0958 0.3459 0.5583 7 M 0.2828 0.2151 0.5021 8 I 0.2642 0.2517 0.4841 9 I 0.0964 0.6779 0.2257 10 A 0.0503 0.8076 0.1421 11 D 0.0501 0.8526 0.0973 12 V 0.0684 0.8132 0.1185 13 L 0.0656 0.7544 0.1800 14 Q 0.0606 0.6001 0.3393 15 M 0.1326 0.3772 0.4903 16 D 0.1657 0.0951 0.7391 17 R 0.0303 0.5158 0.4540 18 G 0.0303 0.4197 0.5500 19 T 0.0921 0.4129 0.4950 20 A 0.1240 0.5667 0.3092 21 P 0.0880 0.7569 0.1551 22 I 0.1136 0.7482 0.1382 23 F 0.1135 0.7487 0.1378 24 I 0.1154 0.7160 0.1685 25 N 0.1144 0.5920 0.2936 26 N 0.0796 0.2543 0.6660 27 G 0.0760 0.1038 0.8202 28 M 0.2010 0.1043 0.6946 29 H 0.2464 0.1468 0.6068 30 C 0.3131 0.1654 0.5215 31 L 0.2120 0.1865 0.6016 32 G 0.1806 0.1130 0.7064 33 C 0.2217 0.0678 0.7105 34 P 0.1268 0.2836 0.5896 35 S 0.1231 0.3666 0.5103 36 S 0.1332 0.3343 0.5325 37 M 0.0969 0.3892 0.5138 38 G 0.0886 0.4153 0.4962 39 E 0.1571 0.3871 0.4558 40 S 0.1456 0.3401 0.5143 41 I 0.0158 0.7642 0.2200 42 E 0.0092 0.8679 0.1229 43 D 0.0086 0.9139 0.0775 44 A 0.0103 0.9088 0.0809 45 C 0.0105 0.8930 0.0965 46 A 0.0161 0.8353 0.1486 47 V 0.0299 0.7053 0.2648 48 H 0.0647 0.2648 0.6704 49 G 0.0569 0.1206 0.8225 50 I 0.1832 0.0768 0.7400 51 D 0.1717 0.0416 0.7868 52 A 0.0146 0.7440 0.2414 53 D 0.0101 0.8588 0.1311 54 K 0.0085 0.9190 0.0725 55 L 0.0088 0.9183 0.0729 56 V 0.0084 0.9169 0.0747 57 K 0.0083 0.9208 0.0709 58 E 0.0085 0.9153 0.0762 59 L 0.0093 0.9063 0.0844 60 N 0.0087 0.9011 0.0902 61 E 0.0086 0.8989 0.0925 62 Y 0.0097 0.8814 0.1088 63 F 0.0133 0.8694 0.1172 64 E 0.0163 0.8250 0.1587 65 K 0.0387 0.6895 0.2718 66 K 0.0775 0.4801 0.4424 67 E 0.1074 0.3347 0.5579 68 V 0.1417 0.2305 0.6278