# This file is the result of combining several RDB files, specifically # T0484.t06.str2.rdb (weight 1.54425) # T0484.t06.str4.rdb (weight 0.924988) # T0484.t06.pb.rdb (weight 0.789901) # T0484.t06.bys.rdb (weight 0.748322) # T0484.t06.alpha.rdb (weight 0.678173) # T0484.t04.str2.rdb (weight 1.54425) # T0484.t04.str4.rdb (weight 0.924988) # T0484.t04.pb.rdb (weight 0.789901) # T0484.t04.bys.rdb (weight 0.748322) # T0484.t04.alpha.rdb (weight 0.678173) # T0484.t2k.str2.rdb (weight 1.54425) # T0484.t2k.str4.rdb (weight 0.924988) # T0484.t2k.pb.rdb (weight 0.789901) # T0484.t2k.bys.rdb (weight 0.748322) # T0484.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 T0484.t06.str2.rdb # ============================================ # TARGET T0484 # 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 T0484.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 23.0267 # # ============================================ # Comments from T0484.t06.str4.rdb # ============================================ # TARGET T0484 # 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 T0484.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 23.0267 # # ============================================ # Comments from T0484.t06.pb.rdb # ============================================ # TARGET T0484 # 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 T0484.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 23.0267 # # ============================================ # Comments from T0484.t06.bys.rdb # ============================================ # TARGET T0484 # 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 T0484.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 23.0267 # # ============================================ # Comments from T0484.t06.alpha.rdb # ============================================ # TARGET T0484 # 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 T0484.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 23.0267 # # ============================================ # Comments from T0484.t04.str2.rdb # ============================================ # TARGET T0484 # 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 T0484.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 24.982 # # ============================================ # Comments from T0484.t04.str4.rdb # ============================================ # TARGET T0484 # 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 T0484.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 24.982 # # ============================================ # Comments from T0484.t04.pb.rdb # ============================================ # TARGET T0484 # 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 T0484.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 24.982 # # ============================================ # Comments from T0484.t04.bys.rdb # ============================================ # TARGET T0484 # 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 T0484.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 24.982 # # ============================================ # Comments from T0484.t04.alpha.rdb # ============================================ # TARGET T0484 # 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 T0484.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 24.982 # # ============================================ # Comments from T0484.t2k.str2.rdb # ============================================ # TARGET T0484 # 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 T0484.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 4.42061 # # ============================================ # Comments from T0484.t2k.str4.rdb # ============================================ # TARGET T0484 # 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 T0484.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 4.42061 # # ============================================ # Comments from T0484.t2k.pb.rdb # ============================================ # TARGET T0484 # 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 T0484.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 4.42061 # # ============================================ # Comments from T0484.t2k.bys.rdb # ============================================ # TARGET T0484 # 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 T0484.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 4.42061 # # ============================================ # Comments from T0484.t2k.alpha.rdb # ============================================ # TARGET T0484 # 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 T0484.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 4.42061 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.2267 0.1975 0.5758 2 R 0.1877 0.2551 0.5573 3 D 0.1804 0.2718 0.5478 4 M 0.1661 0.3095 0.5244 5 T 0.1544 0.3212 0.5244 6 E 0.0941 0.5485 0.3574 7 E 0.1095 0.5426 0.3479 8 T 0.1240 0.4720 0.4040 9 R 0.1010 0.4803 0.4188 10 K 0.0695 0.4545 0.4760 11 D 0.0860 0.2420 0.6720 12 L 0.1756 0.0825 0.7419 13 P 0.1377 0.0648 0.7974 14 P 0.0128 0.7432 0.2440 15 E 0.0095 0.8613 0.1291 16 A 0.0090 0.9138 0.0771 17 L 0.0085 0.9183 0.0732 18 R 0.0083 0.9066 0.0851 19 A 0.0086 0.8934 0.0980 20 L 0.0088 0.8898 0.1014 21 A 0.0086 0.8909 0.1005 22 E 0.0091 0.8769 0.1141 23 A 0.0099 0.8897 0.1004 24 E 0.0085 0.9082 0.0832 25 E 0.0087 0.9099 0.0814 26 R 0.0115 0.9001 0.0883 27 R 0.0109 0.9034 0.0857 28 R 0.0099 0.9014 0.0887 29 R 0.0132 0.8792 0.1075 30 A 0.0161 0.8583 0.1256 31 K 0.0200 0.7987 0.1814 32 A 0.0359 0.6340 0.3301 33 L 0.0846 0.4209 0.4944 34 D 0.1202 0.1973 0.6825 35 L 0.2244 0.0531 0.7224 36 P 0.1930 0.1722 0.6348 37 K 0.1641 0.4274 0.4085 38 E 0.1994 0.3515 0.4491 39 I 0.2132 0.1968 0.5900 40 G 0.1433 0.1141 0.7426 41 G 0.1581 0.0866 0.7552 42 R 0.1733 0.1557 0.6710 43 N 0.1723 0.1105 0.7172 44 G 0.1729 0.0699 0.7572 45 P 0.2126 0.1421 0.6453 46 E 0.3264 0.0858 0.5878 47 P 0.3608 0.1281 0.5111 48 V 0.3799 0.1013 0.5187 49 R 0.3611 0.1232 0.5157 50 F 0.2872 0.1416 0.5712 51 G 0.2057 0.1062 0.6881 52 D 0.2334 0.1162 0.6504 53 W 0.1757 0.4313 0.3931 54 E 0.1996 0.4086 0.3918 55 K 0.2825 0.2738 0.4438 56 K 0.2349 0.1458 0.6194 57 G 0.2767 0.0832 0.6400 58 I 0.5378 0.0673 0.3949 59 A 0.6223 0.0658 0.3120 60 I 0.6161 0.0680 0.3159 61 D 0.4176 0.0743 0.5080 62 F 0.2361 0.1781 0.5857