# This file is the result of combining several RDB files, specifically # T0419.t2k.str2.rdb (weight 1.54425) # T0419.t2k.str4.rdb (weight 0.924988) # T0419.t2k.pb.rdb (weight 0.789901) # T0419.t2k.bys.rdb (weight 0.748322) # T0419.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 T0419.t2k.str2.rdb # ============================================ # TARGET T0419 # 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 T0419.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 4.6763 # # ============================================ # Comments from T0419.t2k.str4.rdb # ============================================ # TARGET T0419 # 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 T0419.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 4.6763 # # ============================================ # Comments from T0419.t2k.pb.rdb # ============================================ # TARGET T0419 # 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 T0419.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 4.6763 # # ============================================ # Comments from T0419.t2k.bys.rdb # ============================================ # TARGET T0419 # 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 T0419.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 4.6763 # # ============================================ # Comments from T0419.t2k.alpha.rdb # ============================================ # TARGET T0419 # 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 T0419.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 4.6763 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 K 0.2009 0.1634 0.6357 2 E 0.1223 0.4347 0.4431 3 R 0.1250 0.4697 0.4053 4 A 0.1441 0.4624 0.3936 5 K 0.1589 0.3756 0.4655 6 R 0.2154 0.2335 0.5511 7 Q 0.2393 0.0754 0.6853 8 P 0.1832 0.1693 0.6476 9 H 0.1878 0.1658 0.6465 10 A 0.2640 0.1471 0.5889 11 A 0.2706 0.1054 0.6240 12 P 0.2622 0.1760 0.5618 13 L 0.3000 0.2024 0.4976 14 V 0.3362 0.2059 0.4579 15 S 0.3087 0.1760 0.5153 16 S 0.2470 0.2103 0.5428 17 L 0.1518 0.3448 0.5034 18 D 0.1231 0.3056 0.5713 19 N 0.0679 0.5166 0.4155 20 R 0.0569 0.6080 0.3352 21 G 0.0712 0.5805 0.3484 22 L 0.0766 0.6157 0.3076 23 L 0.0970 0.5878 0.3153 24 D 0.0638 0.6051 0.3311 25 S 0.0734 0.5882 0.3384 26 L 0.1314 0.5508 0.3179 27 D 0.1210 0.5294 0.3496 28 L 0.0714 0.6504 0.2782 29 G 0.0586 0.6751 0.2664 30 Q 0.0649 0.7001 0.2350 31 Y 0.1024 0.5289 0.3688 32 L 0.1876 0.3413 0.4711 33 D 0.1539 0.1864 0.6597 34 K 0.0192 0.7000 0.2808 35 D 0.0139 0.8217 0.1644 36 A 0.0159 0.8466 0.1374 37 Y 0.0153 0.8869 0.0978 38 K 0.0096 0.9115 0.0789 39 E 0.0084 0.9190 0.0726 40 Q 0.0086 0.9151 0.0763 41 L 0.0088 0.9132 0.0780 42 A 0.0086 0.9156 0.0758 43 A 0.0086 0.9059 0.0855 44 E 0.0084 0.9185 0.0731 45 Q 0.0089 0.9121 0.0790 46 A 0.0101 0.9131 0.0768 47 R 0.0125 0.8989 0.0886 48 L 0.0172 0.8463 0.1365 49 A 0.0239 0.6955 0.2805 50 G 0.0241 0.4493 0.5266 51 L 0.0478 0.5866 0.3655 52 I 0.1052 0.5181 0.3767 53 R 0.1166 0.4974 0.3860 54 D 0.1351 0.4495 0.4153 55 K 0.0323 0.7313 0.2365 56 R 0.0427 0.6946 0.2627 57 F 0.0686 0.6473 0.2841 58 R 0.1127 0.5445 0.3428 59 Q 0.1417 0.3722 0.4861 60 H 0.1546 0.1825 0.6629