# This file is the result of combining several RDB files, specifically # TR464.t04.str2.rdb (weight 1.54425) # TR464.t04.str4.rdb (weight 0.924988) # TR464.t04.pb.rdb (weight 0.789901) # TR464.t04.bys.rdb (weight 0.748322) # TR464.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 TR464.t04.str2.rdb # ============================================ # TARGET TR464 # 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 TR464.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 3.69861 # # ============================================ # Comments from TR464.t04.str4.rdb # ============================================ # TARGET TR464 # 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 TR464.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 3.69861 # # ============================================ # Comments from TR464.t04.pb.rdb # ============================================ # TARGET TR464 # 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 TR464.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 3.69861 # # ============================================ # Comments from TR464.t04.bys.rdb # ============================================ # TARGET TR464 # 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 TR464.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 3.69861 # # ============================================ # Comments from TR464.t04.alpha.rdb # ============================================ # TARGET TR464 # 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 TR464.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 3.69861 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 L 0.3343 0.0657 0.6001 2 S 0.3124 0.0641 0.6235 3 L 0.2524 0.3089 0.4387 4 L 0.1789 0.3990 0.4221 5 E 0.1203 0.4614 0.4183 6 S 0.0585 0.6051 0.3364 7 K 0.0350 0.5710 0.3940 8 G 0.0408 0.5892 0.3700 9 L 0.0178 0.8067 0.1755 10 E 0.0116 0.8904 0.0979 11 A 0.0099 0.9032 0.0869 12 L 0.0121 0.8820 0.1059 13 N 0.0112 0.8828 0.1060 14 K 0.0088 0.8954 0.0958 15 A 0.0115 0.8816 0.1069 16 I 0.0227 0.8116 0.1657 17 A 0.0326 0.6902 0.2772 18 S 0.0709 0.2772 0.6519 19 G 0.0923 0.1367 0.7710 20 T 0.2786 0.1081 0.6134 21 V 0.4587 0.1144 0.4269 22 Q 0.4950 0.1159 0.3891 23 R 0.4719 0.1234 0.4047 24 A 0.3213 0.1923 0.4864 25 D 0.1965 0.1249 0.6786 26 G 0.1154 0.1241 0.7605 27 S 0.2407 0.1000 0.6593 28 I 0.2988 0.1900 0.5112 29 Q 0.2405 0.2301 0.5293 30 N 0.2220 0.1880 0.5901 31 Q 0.2691 0.1252 0.6057 32 S 0.2549 0.1470 0.5982 33 L 0.1338 0.4759 0.3904 34 H 0.1176 0.5602 0.3222 35 E 0.1825 0.5479 0.2696 36 A 0.3134 0.4011 0.2856 37 L 0.4634 0.2608 0.2758 38 I 0.5595 0.1258 0.3147 39 T 0.3794 0.0946 0.5260 40 R 0.2426 0.2003 0.5571 41 D 0.1727 0.1723 0.6550 42 R 0.1110 0.3043 0.5847 43 K 0.2103 0.2232 0.5665 44 Q 0.4703 0.1063 0.4234 45 V 0.6463 0.0302 0.3235 46 F 0.6998 0.0166 0.2836 47 R 0.6910 0.0127 0.2964 48 I 0.5057 0.0537 0.4406 49 E 0.2953 0.1657 0.5390 50 D 0.1747 0.1335 0.6919 51 S 0.1584 0.0957 0.7458 52 I 0.3831 0.0414 0.5755 53 P 0.5425 0.0373 0.4202 54 V 0.6455 0.0405 0.3139 55 L 0.5876 0.0433 0.3691 56 L 0.3505 0.0470 0.6026 57 P 0.1472 0.4021 0.4507 58 E 0.0569 0.6783 0.2648 59 E 0.0458 0.7101 0.2441 60 A 0.0769 0.6786 0.2445 61 I 0.1084 0.6308 0.2608 62 A 0.0896 0.6420 0.2684 63 T 0.0615 0.7263 0.2123 64 I 0.0583 0.7631 0.1786 65 Q 0.0694 0.7518 0.1788 66 I 0.0972 0.6465 0.2563 67 A 0.1219 0.4688 0.4094 68 N 0.1151 0.3067 0.5782 69 F 0.1344 0.2301 0.6354