# This file is the result of combining several RDB files, specifically # T0498.t04.str2.rdb (weight 1.54425) # T0498.t04.str4.rdb (weight 0.924988) # T0498.t04.pb.rdb (weight 0.789901) # T0498.t04.bys.rdb (weight 0.748322) # T0498.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 T0498.t04.str2.rdb # ============================================ # TARGET T0498 # 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 T0498.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 3.77508 # # ============================================ # Comments from T0498.t04.str4.rdb # ============================================ # TARGET T0498 # 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 T0498.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 3.77508 # # ============================================ # Comments from T0498.t04.pb.rdb # ============================================ # TARGET T0498 # 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 T0498.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 3.77508 # # ============================================ # Comments from T0498.t04.bys.rdb # ============================================ # TARGET T0498 # 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 T0498.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 3.77508 # # ============================================ # Comments from T0498.t04.alpha.rdb # ============================================ # TARGET T0498 # 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 T0498.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 3.77508 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 T 0.3839 0.0633 0.5529 2 T 0.5222 0.0457 0.4321 3 Y 0.6960 0.0269 0.2771 4 K 0.7681 0.0184 0.2136 5 L 0.8023 0.0104 0.1873 6 I 0.7996 0.0129 0.1876 7 L 0.7272 0.0233 0.2495 8 N 0.5206 0.0562 0.4232 9 L 0.2732 0.1836 0.5432 10 K 0.1771 0.3423 0.4806 11 Q 0.1828 0.3799 0.4373 12 A 0.1498 0.4416 0.4086 13 K 0.0905 0.5780 0.3315 14 E 0.0454 0.7491 0.2055 15 E 0.0521 0.7853 0.1626 16 A 0.0672 0.7708 0.1619 17 I 0.0543 0.7728 0.1729 18 K 0.0506 0.7796 0.1698 19 E 0.0604 0.7585 0.1811 20 L 0.0628 0.7533 0.1839 21 V 0.1447 0.5851 0.2702 22 D 0.1065 0.5022 0.3913 23 A 0.0250 0.7393 0.2358 24 G 0.0168 0.8290 0.1542 25 T 0.0183 0.8751 0.1066 26 A 0.0092 0.9062 0.0846 27 E 0.0084 0.9187 0.0729 28 K 0.0083 0.9223 0.0694 29 Y 0.0086 0.9216 0.0698 30 I 0.0085 0.9181 0.0734 31 K 0.0083 0.9204 0.0712 32 L 0.0093 0.9165 0.0743 33 I 0.0139 0.8864 0.0998 34 A 0.0327 0.7864 0.1808 35 N 0.0502 0.5446 0.4052 36 A 0.0561 0.3928 0.5511 37 K 0.0845 0.1981 0.7175 38 T 0.1559 0.1111 0.7330 39 V 0.3238 0.0662 0.6099 40 E 0.2887 0.0907 0.6206 41 G 0.3916 0.0560 0.5524 42 V 0.5406 0.0504 0.4090 43 W 0.6394 0.0365 0.3241 44 T 0.5692 0.0411 0.3897 45 L 0.4224 0.1225 0.4551 46 K 0.2365 0.2767 0.4867 47 D 0.1699 0.3616 0.4686 48 E 0.2505 0.2932 0.4563 49 I 0.4101 0.1608 0.4291 50 K 0.5807 0.1037 0.3155 51 T 0.6624 0.0363 0.3013 52 F 0.6706 0.0268 0.3026 53 T 0.6690 0.0212 0.3098 54 V 0.5887 0.0404 0.3710 55 T 0.4271 0.0582 0.5147 56 E 0.3092 0.1482 0.5426