# This file is the result of combining several RDB files, specifically # T0498.t2k.str2.rdb (weight 1.54425) # T0498.t2k.str4.rdb (weight 0.924988) # T0498.t2k.pb.rdb (weight 0.789901) # T0498.t2k.bys.rdb (weight 0.748322) # T0498.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 T0498.t2k.str2.rdb # ============================================ # TARGET T0498 # 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 T0498.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 4.05862 # # ============================================ # Comments from T0498.t2k.str4.rdb # ============================================ # TARGET T0498 # 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 T0498.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 4.05862 # # ============================================ # Comments from T0498.t2k.pb.rdb # ============================================ # TARGET T0498 # 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 T0498.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 4.05862 # # ============================================ # Comments from T0498.t2k.bys.rdb # ============================================ # TARGET T0498 # 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 T0498.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 4.05862 # # ============================================ # Comments from T0498.t2k.alpha.rdb # ============================================ # TARGET T0498 # 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 T0498.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 4.05862 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 T 0.4573 0.0658 0.4769 2 T 0.5934 0.0445 0.3621 3 Y 0.7255 0.0267 0.2479 4 K 0.7845 0.0150 0.2004 5 L 0.7875 0.0118 0.2007 6 I 0.7784 0.0200 0.2016 7 L 0.7248 0.0432 0.2320 8 N 0.5653 0.0603 0.3744 9 L 0.3068 0.2027 0.4905 10 K 0.2137 0.3115 0.4748 11 Q 0.2298 0.3008 0.4694 12 A 0.1883 0.3569 0.4548 13 K 0.1464 0.4817 0.3719 14 E 0.1011 0.6532 0.2457 15 E 0.0971 0.7066 0.1963 16 A 0.1294 0.6709 0.1998 17 I 0.0998 0.6930 0.2072 18 K 0.0792 0.7311 0.1896 19 E 0.0775 0.7165 0.2059 20 L 0.0933 0.6535 0.2532 21 V 0.1417 0.5762 0.2821 22 D 0.1125 0.5100 0.3775 23 A 0.0179 0.7527 0.2295 24 G 0.0131 0.7860 0.2009 25 T 0.0157 0.8272 0.1572 26 A 0.0092 0.8990 0.0919 27 E 0.0084 0.9172 0.0744 28 K 0.0083 0.9217 0.0700 29 Y 0.0085 0.9179 0.0736 30 I 0.0084 0.9191 0.0725 31 K 0.0086 0.9179 0.0735 32 L 0.0102 0.9041 0.0858 33 I 0.0232 0.8314 0.1454 34 A 0.0442 0.6931 0.2627 35 N 0.0722 0.4481 0.4797 36 A 0.0611 0.3310 0.6079 37 K 0.0678 0.1949 0.7373 38 T 0.1528 0.0830 0.7642 39 V 0.3278 0.0681 0.6041 40 E 0.4097 0.0844 0.5059 41 G 0.4631 0.0677 0.4691 42 V 0.6158 0.0453 0.3389 43 W 0.6739 0.0342 0.2919 44 T 0.6199 0.0411 0.3390 45 L 0.4730 0.1114 0.4156 46 K 0.2144 0.3360 0.4496 47 D 0.1444 0.3900 0.4656 48 E 0.1896 0.3849 0.4254 49 I 0.3248 0.2606 0.4146 50 K 0.3682 0.1667 0.4651 51 T 0.4715 0.0821 0.4464 52 F 0.5123 0.0456 0.4421 53 T 0.5830 0.0311 0.3859 54 V 0.5063 0.0633 0.4304 55 T 0.3513 0.0608 0.5879 56 E 0.2511 0.2295 0.5194