# This file is the result of combining several RDB files, specifically # T0492.t04.str2.rdb (weight 1.54425) # T0492.t04.str4.rdb (weight 0.924988) # T0492.t04.pb.rdb (weight 0.789901) # T0492.t04.bys.rdb (weight 0.748322) # T0492.t04.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 T0492.t04.str2.rdb # ============================================ # TARGET T0492 # 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 T0492.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 61.0248 # # ============================================ # Comments from T0492.t04.str4.rdb # ============================================ # TARGET T0492 # 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 T0492.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 61.0248 # # ============================================ # Comments from T0492.t04.pb.rdb # ============================================ # TARGET T0492 # 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 T0492.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 61.0248 # # ============================================ # Comments from T0492.t04.bys.rdb # ============================================ # TARGET T0492 # 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 T0492.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 61.0248 # # ============================================ # Comments from T0492.t04.alpha.rdb # ============================================ # TARGET T0492 # 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 T0492.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 61.0248 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.3259 0.0910 0.5831 2 F 0.4137 0.0408 0.5455 3 S 0.3523 0.0360 0.6117 4 L 0.1614 0.4223 0.4163 5 R 0.1270 0.4725 0.4004 6 D 0.1669 0.2887 0.5444 7 A 0.2908 0.0991 0.6101 8 K 0.2563 0.0993 0.6444 9 C 0.1539 0.1193 0.7267 10 G 0.0917 0.0918 0.8166 11 Q 0.4029 0.0285 0.5686 12 T 0.6851 0.0149 0.3000 13 V 0.7825 0.0069 0.2106 14 K 0.8023 0.0059 0.1918 15 V 0.7464 0.0050 0.2487 16 V 0.7348 0.0133 0.2520 17 K 0.7540 0.0104 0.2356 18 L 0.6214 0.0336 0.3450 19 H 0.3800 0.0700 0.5501 20 G 0.1859 0.1417 0.6723 21 T 0.1037 0.2510 0.6454 22 G 0.0467 0.4621 0.4912 23 A 0.0280 0.7593 0.2128 24 L 0.0183 0.8713 0.1104 25 K 0.0100 0.9084 0.0816 26 R 0.0101 0.9153 0.0746 27 R 0.0123 0.9092 0.0785 28 I 0.0113 0.8969 0.0918 29 M 0.0129 0.8877 0.0994 30 D 0.0241 0.7595 0.2164 31 M 0.0762 0.3831 0.5407 32 G 0.1002 0.1518 0.7479 33 I 0.2182 0.0977 0.6841 34 T 0.2908 0.0421 0.6670 35 R 0.1328 0.1619 0.7053 36 G 0.0677 0.1106 0.8217 37 C 0.3724 0.0242 0.6034 38 E 0.6665 0.0116 0.3219 39 I 0.7856 0.0066 0.2078 40 Y 0.7829 0.0079 0.2091 41 I 0.7381 0.0063 0.2556 42 R 0.7153 0.0259 0.2588 43 K 0.7065 0.0249 0.2686 44 V 0.5937 0.0468 0.3595 45 A 0.4012 0.0316 0.5672 46 P 0.2740 0.1104 0.6156 47 L 0.1486 0.1335 0.7179 48 G 0.1162 0.0753 0.8084 49 D 0.2337 0.0235 0.7428 50 P 0.4184 0.0596 0.5220 51 I 0.7034 0.0306 0.2659 52 Q 0.7983 0.0067 0.1951 53 I 0.8114 0.0053 0.1833 54 N 0.7712 0.0061 0.2226 55 V 0.7053 0.0224 0.2723 56 R 0.3709 0.0715 0.5575 57 G 0.1746 0.0792 0.7463 58 Y 0.4462 0.0833 0.4706 59 E 0.5962 0.1239 0.2798 60 L 0.5985 0.1976 0.2038 61 S 0.5612 0.2200 0.2187 62 L 0.5292 0.2233 0.2474 63 R 0.2659 0.3070 0.4271 64 K 0.0920 0.5977 0.3103 65 S 0.0532 0.6712 0.2756 66 A 0.0611 0.6428 0.2961 67 A 0.1792 0.4711 0.3497 68 E 0.1677 0.4102 0.4221 69 M 0.4700 0.1484 0.3816 70 I 0.5994 0.0507 0.3500 71 E 0.7000 0.0236 0.2764 72 V 0.6827 0.0252 0.2920 73 E 0.4490 0.0467 0.5043