# This file is the result of combining several RDB files, specifically # T0472.t06.str2.rdb (weight 1.54425) # T0472.t06.str4.rdb (weight 0.924988) # T0472.t06.pb.rdb (weight 0.789901) # T0472.t06.bys.rdb (weight 0.748322) # T0472.t06.alpha.rdb (weight 0.678173) # T0472.t04.str2.rdb (weight 1.54425) # T0472.t04.str4.rdb (weight 0.924988) # T0472.t04.pb.rdb (weight 0.789901) # T0472.t04.bys.rdb (weight 0.748322) # T0472.t04.alpha.rdb (weight 0.678173) # T0472.t2k.str2.rdb (weight 1.54425) # T0472.t2k.str4.rdb (weight 0.924988) # T0472.t2k.pb.rdb (weight 0.789901) # T0472.t2k.bys.rdb (weight 0.748322) # T0472.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 T0472.t06.str2.rdb # ============================================ # TARGET T0472 # 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 T0472.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 17.5964 # # ============================================ # Comments from T0472.t06.str4.rdb # ============================================ # TARGET T0472 # 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 T0472.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 17.5964 # # ============================================ # Comments from T0472.t06.pb.rdb # ============================================ # TARGET T0472 # 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 T0472.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 17.5964 # # ============================================ # Comments from T0472.t06.bys.rdb # ============================================ # TARGET T0472 # 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 T0472.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 17.5964 # # ============================================ # Comments from T0472.t06.alpha.rdb # ============================================ # TARGET T0472 # 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 T0472.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 17.5964 # # ============================================ # Comments from T0472.t04.str2.rdb # ============================================ # TARGET T0472 # 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 T0472.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 15.5899 # # ============================================ # Comments from T0472.t04.str4.rdb # ============================================ # TARGET T0472 # 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 T0472.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 15.5899 # # ============================================ # Comments from T0472.t04.pb.rdb # ============================================ # TARGET T0472 # 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 T0472.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 15.5899 # # ============================================ # Comments from T0472.t04.bys.rdb # ============================================ # TARGET T0472 # 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 T0472.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 15.5899 # # ============================================ # Comments from T0472.t04.alpha.rdb # ============================================ # TARGET T0472 # 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 T0472.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 15.5899 # # ============================================ # Comments from T0472.t2k.str2.rdb # ============================================ # TARGET T0472 # 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 T0472.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 12.8112 # # ============================================ # Comments from T0472.t2k.str4.rdb # ============================================ # TARGET T0472 # 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 T0472.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 12.8112 # # ============================================ # Comments from T0472.t2k.pb.rdb # ============================================ # TARGET T0472 # 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 T0472.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 12.8112 # # ============================================ # Comments from T0472.t2k.bys.rdb # ============================================ # TARGET T0472 # 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 T0472.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 12.8112 # # ============================================ # Comments from T0472.t2k.alpha.rdb # ============================================ # TARGET T0472 # 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 T0472.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 12.8112 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.2748 0.1392 0.5859 2 S 0.2552 0.1101 0.6347 3 G 0.3037 0.1023 0.5940 4 W 0.6116 0.0789 0.3095 5 Y 0.7011 0.0452 0.2537 6 E 0.7499 0.0258 0.2242 7 L 0.7411 0.0311 0.2278 8 S 0.6739 0.0407 0.2854 9 K 0.5540 0.0901 0.3559 10 S 0.3035 0.1018 0.5947 11 S 0.1496 0.2320 0.6184 12 N 0.1006 0.1648 0.7345 13 D 0.1530 0.0966 0.7504 14 Q 0.4558 0.0294 0.5148 15 F 0.6925 0.0129 0.2946 16 K 0.7813 0.0097 0.2090 17 F 0.8176 0.0054 0.1769 18 V 0.8193 0.0050 0.1757 19 L 0.7965 0.0066 0.1969 20 K 0.7232 0.0123 0.2645 21 A 0.4607 0.0348 0.5045 22 G 0.2904 0.0680 0.6416 23 N 0.1535 0.0874 0.7591 24 G 0.1538 0.0851 0.7611 25 E 0.5312 0.0275 0.4413 26 V 0.7069 0.0118 0.2814 27 I 0.7609 0.0163 0.2229 28 L 0.7385 0.0229 0.2386 29 T 0.6379 0.0487 0.3134 30 S 0.4786 0.0908 0.4306 31 E 0.2893 0.2990 0.4117 32 L 0.2388 0.3324 0.4288 33 Y 0.2610 0.2875 0.4514 34 T 0.1854 0.3236 0.4910 35 G 0.1292 0.3444 0.5265 36 K 0.0560 0.6429 0.3011 37 S 0.0503 0.6538 0.2958 38 G 0.0508 0.6689 0.2803 39 A 0.0463 0.7654 0.1884 40 M 0.0517 0.6991 0.2491 41 N 0.0485 0.5663 0.3852 42 G 0.0798 0.4886 0.4316 43 I 0.0908 0.6651 0.2440 44 E 0.0915 0.7244 0.1841 45 S 0.1316 0.6844 0.1841 46 V 0.1034 0.7094 0.1872 47 Q 0.1228 0.6121 0.2651 48 T 0.1071 0.4334 0.4595 49 N 0.1039 0.2136 0.6824 50 S 0.1668 0.1175 0.7157 51 P 0.1482 0.2608 0.5909 52 I 0.1011 0.4425 0.4564 53 E 0.0967 0.4671 0.4362 54 A 0.1225 0.3206 0.5568 55 R 0.1461 0.2146 0.6393