# This file is the result of combining several RDB files, specifically # T0476.t06.str2.rdb (weight 1.54425) # T0476.t06.str4.rdb (weight 0.924988) # T0476.t06.pb.rdb (weight 0.789901) # T0476.t06.bys.rdb (weight 0.748322) # T0476.t06.alpha.rdb (weight 0.678173) # T0476.t04.str2.rdb (weight 1.54425) # T0476.t04.str4.rdb (weight 0.924988) # T0476.t04.pb.rdb (weight 0.789901) # T0476.t04.bys.rdb (weight 0.748322) # T0476.t04.alpha.rdb (weight 0.678173) # T0476.t2k.str2.rdb (weight 1.54425) # T0476.t2k.str4.rdb (weight 0.924988) # T0476.t2k.pb.rdb (weight 0.789901) # T0476.t2k.bys.rdb (weight 0.748322) # T0476.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 T0476.t06.str2.rdb # ============================================ # TARGET T0476 # 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 T0476.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 2.33036 # # ============================================ # Comments from T0476.t06.str4.rdb # ============================================ # TARGET T0476 # 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 T0476.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 2.33036 # # ============================================ # Comments from T0476.t06.pb.rdb # ============================================ # TARGET T0476 # 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 T0476.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 2.33036 # # ============================================ # Comments from T0476.t06.bys.rdb # ============================================ # TARGET T0476 # 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 T0476.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 2.33036 # # ============================================ # Comments from T0476.t06.alpha.rdb # ============================================ # TARGET T0476 # 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 T0476.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 2.33036 # # ============================================ # Comments from T0476.t04.str2.rdb # ============================================ # TARGET T0476 # 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 T0476.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 2.33036 # # ============================================ # Comments from T0476.t04.str4.rdb # ============================================ # TARGET T0476 # 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 T0476.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 2.33036 # # ============================================ # Comments from T0476.t04.pb.rdb # ============================================ # TARGET T0476 # 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 T0476.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 2.33036 # # ============================================ # Comments from T0476.t04.bys.rdb # ============================================ # TARGET T0476 # 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 T0476.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 2.33036 # # ============================================ # Comments from T0476.t04.alpha.rdb # ============================================ # TARGET T0476 # 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 T0476.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 2.33036 # # ============================================ # Comments from T0476.t2k.str2.rdb # ============================================ # TARGET T0476 # 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 T0476.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 2.33065 # # ============================================ # Comments from T0476.t2k.str4.rdb # ============================================ # TARGET T0476 # 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 T0476.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 2.33065 # # ============================================ # Comments from T0476.t2k.pb.rdb # ============================================ # TARGET T0476 # 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 T0476.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 2.33065 # # ============================================ # Comments from T0476.t2k.bys.rdb # ============================================ # TARGET T0476 # 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 T0476.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 2.33065 # # ============================================ # Comments from T0476.t2k.alpha.rdb # ============================================ # TARGET T0476 # 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 T0476.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 2.33065 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 S 0.2377 0.1584 0.6039 2 A 0.2643 0.1350 0.6007 3 K 0.2941 0.1041 0.6018 4 C 0.3386 0.0679 0.5935 5 P 0.2186 0.1683 0.6132 6 I 0.2353 0.2068 0.5580 7 C 0.1848 0.1629 0.6523 8 G 0.1393 0.1121 0.7487 9 S 0.1927 0.0694 0.7379 10 P 0.1715 0.2012 0.6273 11 L 0.1839 0.2723 0.5439 12 K 0.1340 0.3092 0.5568 13 W 0.0189 0.7705 0.2106 14 E 0.0092 0.8722 0.1186 15 E 0.0083 0.9217 0.0699 16 L 0.0084 0.9200 0.0716 17 I 0.0084 0.9201 0.0715 18 E 0.0084 0.9194 0.0722 19 E 0.0087 0.9089 0.0824 20 M 0.0117 0.8835 0.1048 21 L 0.0186 0.8578 0.1237 22 I 0.0303 0.7984 0.1713 23 I 0.0468 0.7274 0.2258 24 E 0.0426 0.6808 0.2765 25 N 0.0590 0.5789 0.3621 26 F 0.0298 0.7547 0.2156 27 E 0.0151 0.8504 0.1345 28 E 0.0189 0.8529 0.1282 29 I 0.0284 0.8307 0.1409 30 V 0.0328 0.7929 0.1743 31 K 0.0318 0.7734 0.1948 32 D 0.0632 0.6568 0.2800 33 R 0.0139 0.8169 0.1692 34 E 0.0091 0.8939 0.0970 35 R 0.0089 0.9092 0.0819 36 F 0.0101 0.9042 0.0857 37 L 0.0096 0.9016 0.0888 38 A 0.0095 0.8923 0.0982 39 Q 0.0171 0.8094 0.1735 40 V 0.0397 0.7488 0.2115 41 E 0.0431 0.7436 0.2133 42 E 0.0808 0.6337 0.2856 43 F 0.2294 0.4174 0.3531 44 V 0.3802 0.2399 0.3799 45 F 0.4788 0.1141 0.4070 46 K 0.4193 0.0761 0.5046 47 C 0.3162 0.0454 0.6384 48 P 0.1682 0.2126 0.6192 49 V 0.1806 0.2275 0.5919 50 C 0.1752 0.2145 0.6103 51 G 0.1760 0.2665 0.5575 52 E 0.1898 0.4511 0.3591 53 E 0.2165 0.4757 0.3078 54 F 0.2657 0.4076 0.3267 55 Y 0.2212 0.2791 0.4998 56 G 0.1666 0.2126 0.6208 57 K 0.2084 0.2180 0.5736 58 T 0.2649 0.1288 0.6063 59 L 0.2673 0.0484 0.6844 60 P 0.1810 0.0738 0.7452 61 R 0.0593 0.4640 0.4767 62 R 0.0314 0.7183 0.2503 63 E 0.0324 0.7652 0.2023 64 A 0.0233 0.8336 0.1431 65 E 0.0215 0.8609 0.1175 66 K 0.0192 0.8794 0.1013 67 V 0.0201 0.8811 0.0988 68 F 0.0330 0.8661 0.1009 69 E 0.0462 0.8420 0.1118 70 L 0.0708 0.7516 0.1776 71 L 0.0783 0.6559 0.2658 72 N 0.0828 0.5193 0.3980 73 D 0.0890 0.3781 0.5330 74 F 0.1293 0.2915 0.5792 75 K 0.1341 0.2342 0.6316 76 G 0.1317 0.1667 0.7016 77 G 0.2632 0.1064 0.6304 78 I 0.4445 0.0684 0.4871 79 D 0.3009 0.0523 0.6467 80 W 0.1008 0.4547 0.4445 81 E 0.0833 0.3590 0.5577 82 N 0.1389 0.2472 0.6138 83 K 0.2544 0.1646 0.5810 84 R 0.4986 0.0859 0.4155 85 V 0.6279 0.0529 0.3193 86 K 0.7072 0.0392 0.2535 87 L 0.7164 0.0511 0.2325 88 K 0.5621 0.1031 0.3348 89 L 0.2882 0.4122 0.2996 90 N 0.1103 0.6023 0.2874 91 D 0.0493 0.7531 0.1976 92 L 0.0272 0.8513 0.1214 93 L 0.0299 0.8718 0.0984 94 A 0.0235 0.8800 0.0965 95 L 0.0157 0.8916 0.0927 96 E 0.0095 0.8980 0.0925 97 T 0.0102 0.8814 0.1085 98 M 0.0155 0.8521 0.1324 99 L 0.0186 0.8556 0.1258 100 E 0.0145 0.8709 0.1146 101 E 0.0219 0.8283 0.1499 102 W 0.0482 0.7661 0.1857 103 D 0.0515 0.7495 0.1990 104 R 0.0429 0.7671 0.1900 105 R 0.0746 0.6368 0.2886 106 V 0.1354 0.4926 0.3721 107 K 0.1575 0.3227 0.5198 108 R 0.1566 0.2222 0.6212