# This file is the result of combining several RDB files, specifically # T0569.t06.str2.rdb (weight 1.54425) # T0569.t06.str4.rdb (weight 0.924988) # T0569.t06.pb.rdb (weight 0.789901) # T0569.t06.bys.rdb (weight 0.748322) # T0569.t06.alpha.rdb (weight 0.678173) # T0569.t04.str2.rdb (weight 1.54425) # T0569.t04.str4.rdb (weight 0.924988) # T0569.t04.pb.rdb (weight 0.789901) # T0569.t04.bys.rdb (weight 0.748322) # T0569.t04.alpha.rdb (weight 0.678173) # T0569.t2k.str2.rdb (weight 1.54425) # T0569.t2k.str4.rdb (weight 0.924988) # T0569.t2k.pb.rdb (weight 0.789901) # T0569.t2k.bys.rdb (weight 0.748322) # T0569.t2k.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 T0569.t06.str2.rdb # ============================================ # TARGET T0569 # 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 T0569.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 4.52249 # # ============================================ # Comments from T0569.t06.str4.rdb # ============================================ # TARGET T0569 # 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 T0569.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 4.52249 # # ============================================ # Comments from T0569.t06.pb.rdb # ============================================ # TARGET T0569 # 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 T0569.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 4.52249 # # ============================================ # Comments from T0569.t06.bys.rdb # ============================================ # TARGET T0569 # 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 T0569.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 4.52249 # # ============================================ # Comments from T0569.t06.alpha.rdb # ============================================ # TARGET T0569 # 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 T0569.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 4.52249 # # ============================================ # Comments from T0569.t04.str2.rdb # ============================================ # TARGET T0569 # 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 T0569.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 4.52249 # # ============================================ # Comments from T0569.t04.str4.rdb # ============================================ # TARGET T0569 # 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 T0569.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 4.52249 # # ============================================ # Comments from T0569.t04.pb.rdb # ============================================ # TARGET T0569 # 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 T0569.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 4.52249 # # ============================================ # Comments from T0569.t04.bys.rdb # ============================================ # TARGET T0569 # 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 T0569.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 4.52249 # # ============================================ # Comments from T0569.t04.alpha.rdb # ============================================ # TARGET T0569 # 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 T0569.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 4.52249 # # ============================================ # Comments from T0569.t2k.str2.rdb # ============================================ # TARGET T0569 # Using neural net dunbrack-40pc-3157-t2k-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 T0569.t2k-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 3 # # ============================================ # Comments from T0569.t2k.str4.rdb # ============================================ # TARGET T0569 # Using neural net dunbrack-40pc-3157-t2k-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 T0569.t2k-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 3 # # ============================================ # Comments from T0569.t2k.pb.rdb # ============================================ # TARGET T0569 # Using neural net dunbrack-40pc-3157-t2k-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 T0569.t2k-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 3 # # ============================================ # Comments from T0569.t2k.bys.rdb # ============================================ # TARGET T0569 # Using neural net dunbrack-40pc-3157-t2k-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 T0569.t2k-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 3 # # ============================================ # Comments from T0569.t2k.alpha.rdb # ============================================ # TARGET T0569 # Using neural net dunbrack-40pc-3157-t2k-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 T0569.t2k-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 3 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.3218 0.0745 0.6037 2 D 0.2397 0.0435 0.7169 3 E 0.1423 0.3329 0.5248 4 D 0.2195 0.2010 0.5795 5 A 0.4545 0.0526 0.4929 6 T 0.6009 0.0206 0.3785 7 I 0.7103 0.0123 0.2774 8 T 0.7349 0.0152 0.2500 9 Y 0.7585 0.0128 0.2288 10 V 0.6896 0.0276 0.2828 11 D 0.5521 0.0289 0.4190 12 D 0.2717 0.1915 0.5368 13 D 0.1588 0.2448 0.5965 14 K 0.1119 0.1751 0.7129 15 G 0.1019 0.1071 0.7910 16 G 0.2050 0.0704 0.7246 17 A 0.4109 0.0474 0.5417 18 Q 0.5382 0.0521 0.4097 19 V 0.5427 0.0740 0.3833 20 G 0.4921 0.0629 0.4450 21 D 0.5629 0.0465 0.3906 22 I 0.6733 0.0248 0.3019 23 V 0.7214 0.0142 0.2644 24 T 0.6843 0.0108 0.3049 25 V 0.6124 0.0328 0.3548 26 T 0.4057 0.0600 0.5344 27 G 0.2781 0.0684 0.6535 28 K 0.3315 0.0686 0.5999 29 T 0.3161 0.0615 0.6224 30 D 0.2265 0.1453 0.6282 31 D 0.2229 0.1968 0.5803 32 S 0.3318 0.1125 0.5557 33 T 0.4245 0.0667 0.5088 34 T 0.5070 0.0426 0.4504 35 Y 0.5649 0.0441 0.3911 36 T 0.6432 0.0317 0.3251 37 V 0.6926 0.0193 0.2881 38 T 0.6664 0.0152 0.3184 39 I 0.5012 0.0197 0.4791 40 P 0.2980 0.0860 0.6160 41 D 0.1753 0.1126 0.7121 42 G 0.1763 0.0909 0.7328 43 Y 0.5115 0.0354 0.4531 44 E 0.6667 0.0356 0.2977 45 Y 0.7165 0.0242 0.2593 46 V 0.6766 0.0328 0.2906 47 G 0.4885 0.0374 0.4740 48 T 0.2947 0.1514 0.5539 49 D 0.1489 0.1214 0.7297 50 G 0.1821 0.0750 0.7429 51 G 0.3773 0.0372 0.5856 52 V 0.6632 0.0160 0.3208 53 V 0.6672 0.0169 0.3159 54 S 0.5377 0.0251 0.4372 55 S 0.2967 0.1769 0.5264 56 D 0.1250 0.1375 0.7375 57 G 0.0986 0.0792 0.8221 58 K 0.4101 0.0270 0.5628 59 T 0.6188 0.0173 0.3639 60 V 0.6500 0.0198 0.3302 61 T 0.7587 0.0096 0.2317 62 I 0.7720 0.0098 0.2183 63 T 0.7812 0.0095 0.2093 64 F 0.7664 0.0121 0.2214 65 A 0.6659 0.0248 0.3093 66 A 0.4528 0.0590 0.4882 67 D 0.2581 0.0941 0.6477 68 D 0.1960 0.1125 0.6916 69 S 0.1662 0.1934 0.6404 70 D 0.2189 0.1288 0.6523 71 N 0.5337 0.0403 0.4259 72 V 0.7431 0.0088 0.2481 73 V 0.7949 0.0058 0.1993 74 I 0.8158 0.0054 0.1788 75 H 0.7918 0.0061 0.2021 76 L 0.7132 0.0183 0.2685 77 K 0.4875 0.0523 0.4602 78 H 0.2651 0.0708 0.6641 79 G 0.1460 0.0934 0.7606