# This file is the result of combining several RDB files, specifically # T0397.t04.str2.rdb (weight 1.54425) # T0397.t04.str4.rdb (weight 0.924988) # T0397.t04.pb.rdb (weight 0.789901) # T0397.t04.bys.rdb (weight 0.748322) # T0397.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 T0397.t04.str2.rdb # ============================================ # TARGET T0397 # 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 T0397.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 3.87914 # # ============================================ # Comments from T0397.t04.str4.rdb # ============================================ # TARGET T0397 # 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 T0397.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 3.87914 # # ============================================ # Comments from T0397.t04.pb.rdb # ============================================ # TARGET T0397 # 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 T0397.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 3.87914 # # ============================================ # Comments from T0397.t04.bys.rdb # ============================================ # TARGET T0397 # 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 T0397.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 3.87914 # # ============================================ # Comments from T0397.t04.alpha.rdb # ============================================ # TARGET T0397 # 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 T0397.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 3.87914 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 G 0.2019 0.0959 0.7022 2 T 0.3288 0.0875 0.5836 3 K 0.5252 0.0651 0.4097 4 L 0.6622 0.0359 0.3019 5 I 0.7170 0.0213 0.2617 6 S 0.7263 0.0117 0.2621 7 V 0.6660 0.0136 0.3204 8 P 0.4718 0.0194 0.5087 9 A 0.3455 0.1224 0.5321 10 E 0.2034 0.1526 0.6439 11 G 0.1700 0.0929 0.7370 12 Y 0.3823 0.0503 0.5674 13 K 0.5826 0.0378 0.3797 14 V 0.6244 0.0341 0.3416 15 Y 0.5560 0.0294 0.4146 16 P 0.5172 0.0777 0.4051 17 I 0.5093 0.1446 0.3461 18 M 0.4715 0.1414 0.3870 19 D 0.3619 0.1540 0.4842 20 F 0.2063 0.2920 0.5016 21 G 0.1791 0.2417 0.5792 22 F 0.3126 0.3053 0.3820 23 R 0.4434 0.2667 0.2899 24 V 0.4060 0.2805 0.3136 25 L 0.3325 0.2557 0.4118 26 K 0.1675 0.1948 0.6377 27 G 0.1025 0.1158 0.7817 28 Y 0.2835 0.0988 0.6177 29 R 0.4644 0.1322 0.4034 30 L 0.5292 0.1579 0.3129 31 A 0.6514 0.1010 0.2477 32 T 0.7193 0.0536 0.2271 33 L 0.7011 0.0659 0.2331 34 E 0.6289 0.0716 0.2996 35 S 0.4457 0.0666 0.4877 36 K 0.2066 0.2438 0.5495 37 K 0.1538 0.1370 0.7092 38 G 0.2235 0.0721 0.7043 39 D 0.5039 0.0345 0.4616 40 L 0.6972 0.0117 0.2911 41 R 0.7327 0.0157 0.2516 42 Y 0.7529 0.0101 0.2369 43 V 0.6989 0.0251 0.2760 44 N 0.5773 0.0345 0.3882 45 S 0.3991 0.0224 0.5785 46 P 0.2740 0.0707 0.6553 47 V 0.2753 0.1126 0.6121 48 S 0.2253 0.0959 0.6788 49 G 0.3711 0.0401 0.5888 50 T 0.6967 0.0114 0.2918 51 V 0.7858 0.0056 0.2086 52 I 0.8151 0.0055 0.1794 53 F 0.7845 0.0062 0.2092 54 M 0.6874 0.0303 0.2823 55 N 0.5017 0.0559 0.4424 56 E 0.3842 0.0862 0.5296 57 I 0.3013 0.0367 0.6620 58 P 0.1920 0.0843 0.7237 59 S 0.1348 0.2436 0.6216 60 E 0.1286 0.2151 0.6563 61 R 0.2284 0.1219 0.6497 62 A 0.2143 0.2299 0.5558 63 N 0.3509 0.1402 0.5089 64 Y 0.6808 0.0412 0.2780 65 V 0.7566 0.0168 0.2266 66 F 0.8076 0.0104 0.1820 67 Y 0.8147 0.0082 0.1771 68 M 0.7591 0.0187 0.2222 69 L 0.5849 0.0372 0.3780 70 E 0.2914 0.1704 0.5382 71 E 0.1664 0.2607 0.5729