# This file is the result of combining several RDB files, specifically # TR476.t06.str2.rdb (weight 1.54425) # TR476.t06.str4.rdb (weight 0.924988) # TR476.t06.pb.rdb (weight 0.789901) # TR476.t06.bys.rdb (weight 0.748322) # TR476.t06.alpha.rdb (weight 0.678173) # TR476.t04.str2.rdb (weight 1.54425) # TR476.t04.str4.rdb (weight 0.924988) # TR476.t04.pb.rdb (weight 0.789901) # TR476.t04.bys.rdb (weight 0.748322) # TR476.t04.alpha.rdb (weight 0.678173) # TR476.t2k.str2.rdb (weight 1.54425) # TR476.t2k.str4.rdb (weight 0.924988) # TR476.t2k.pb.rdb (weight 0.789901) # TR476.t2k.bys.rdb (weight 0.748322) # TR476.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 TR476.t06.str2.rdb # ============================================ # TARGET TR476 # 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 TR476.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 2.29899 # # ============================================ # Comments from TR476.t06.str4.rdb # ============================================ # TARGET TR476 # 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 TR476.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 2.29899 # # ============================================ # Comments from TR476.t06.pb.rdb # ============================================ # TARGET TR476 # 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 TR476.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 2.29899 # # ============================================ # Comments from TR476.t06.bys.rdb # ============================================ # TARGET TR476 # 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 TR476.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 2.29899 # # ============================================ # Comments from TR476.t06.alpha.rdb # ============================================ # TARGET TR476 # 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 TR476.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 2.29899 # # ============================================ # Comments from TR476.t04.str2.rdb # ============================================ # TARGET TR476 # 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 TR476.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 2.29899 # # ============================================ # Comments from TR476.t04.str4.rdb # ============================================ # TARGET TR476 # 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 TR476.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 2.29899 # # ============================================ # Comments from TR476.t04.pb.rdb # ============================================ # TARGET TR476 # 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 TR476.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 2.29899 # # ============================================ # Comments from TR476.t04.bys.rdb # ============================================ # TARGET TR476 # 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 TR476.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 2.29899 # # ============================================ # Comments from TR476.t04.alpha.rdb # ============================================ # TARGET TR476 # 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 TR476.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 2.29899 # # ============================================ # Comments from TR476.t2k.str2.rdb # ============================================ # TARGET TR476 # 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 TR476.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 2.29899 # # ============================================ # Comments from TR476.t2k.str4.rdb # ============================================ # TARGET TR476 # 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 TR476.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 2.29899 # # ============================================ # Comments from TR476.t2k.pb.rdb # ============================================ # TARGET TR476 # 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 TR476.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 2.29899 # # ============================================ # Comments from TR476.t2k.bys.rdb # ============================================ # TARGET TR476 # 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 TR476.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 2.29899 # # ============================================ # Comments from TR476.t2k.alpha.rdb # ============================================ # TARGET TR476 # 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 TR476.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 2.29899 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 A 0.3203 0.1225 0.5572 2 K 0.3081 0.0903 0.6016 3 C 0.3347 0.0609 0.6044 4 P 0.2169 0.1578 0.6253 5 I 0.2386 0.1946 0.5668 6 C 0.1863 0.1569 0.6568 7 G 0.1433 0.1090 0.7477 8 S 0.1933 0.0677 0.7390 9 P 0.1728 0.1977 0.6295 10 L 0.1843 0.2673 0.5484 11 K 0.1335 0.3048 0.5617 12 W 0.0191 0.7696 0.2113 13 E 0.0092 0.8721 0.1187 14 E 0.0083 0.9217 0.0700 15 L 0.0084 0.9199 0.0717 16 I 0.0084 0.9201 0.0715 17 E 0.0084 0.9194 0.0722 18 E 0.0087 0.9089 0.0824 19 M 0.0117 0.8834 0.1049 20 L 0.0186 0.8578 0.1236 21 I 0.0304 0.7979 0.1717 22 I 0.0468 0.7277 0.2256 23 E 0.0427 0.6814 0.2758 24 N 0.0590 0.5796 0.3613 25 F 0.0297 0.7549 0.2154 26 E 0.0151 0.8501 0.1347 27 E 0.0189 0.8529 0.1282 28 I 0.0284 0.8306 0.1410 29 V 0.0330 0.7925 0.1745 30 K 0.0318 0.7736 0.1946 31 D 0.0629 0.6573 0.2798 32 R 0.0140 0.8167 0.1693 33 E 0.0091 0.8936 0.0973 34 R 0.0089 0.9085 0.0825 35 F 0.0101 0.9036 0.0863 36 L 0.0097 0.9012 0.0891 37 A 0.0096 0.8920 0.0984 38 Q 0.0172 0.8089 0.1739 39 V 0.0401 0.7478 0.2121 40 E 0.0433 0.7433 0.2134 41 E 0.0808 0.6337 0.2855 42 F 0.2294 0.4182 0.3525 43 V 0.3796 0.2402 0.3803 44 F 0.4781 0.1149 0.4070 45 K 0.4191 0.0762 0.5047 46 C 0.3162 0.0454 0.6384 47 P 0.1683 0.2128 0.6189 48 V 0.1806 0.2281 0.5913 49 C 0.1751 0.2149 0.6100 50 G 0.1757 0.2667 0.5576 51 E 0.1890 0.4525 0.3585 52 E 0.2155 0.4766 0.3079 53 F 0.2646 0.4088 0.3267 54 Y 0.2209 0.2794 0.4997 55 G 0.1663 0.2130 0.6208 56 K 0.2084 0.2182 0.5734 57 T 0.2652 0.1290 0.6058 58 L 0.2675 0.0485 0.6839 59 P 0.1811 0.0740 0.7449 60 R 0.0597 0.4627 0.4776 61 R 0.0316 0.7165 0.2519 62 E 0.0327 0.7639 0.2034 63 A 0.0235 0.8331 0.1435 64 E 0.0215 0.8613 0.1172 65 K 0.0194 0.8797 0.1009 66 V 0.0199 0.8814 0.0987 67 F 0.0323 0.8671 0.1007 68 E 0.0451 0.8436 0.1113 69 L 0.0702 0.7536 0.1762 70 L 0.0779 0.6575 0.2646 71 N 0.0824 0.5213 0.3963 72 D 0.0882 0.3796 0.5322 73 F 0.1291 0.2918 0.5791 74 K 0.1341 0.2342 0.6317 75 G 0.1318 0.1661 0.7021 76 G 0.2661 0.1061 0.6279 77 I 0.4490 0.0657 0.4853 78 D 0.3007 0.0499 0.6493 79 W 0.1136 0.4424 0.4440 80 E 0.0994 0.3477 0.5529 81 N 0.1679 0.2292 0.6030 82 K 0.3300 0.1099 0.5601 83 R 0.5479 0.0467 0.4053 84 V 0.6492 0.0201 0.3307 85 K 0.6927 0.0154 0.2919 86 L 0.6614 0.0221 0.3165 87 K 0.3997 0.0357 0.5647