# This file is the result of combining several RDB files, specifically # T0473.t2k.str2.rdb (weight 1.54425) # T0473.t2k.str4.rdb (weight 0.924988) # T0473.t2k.pb.rdb (weight 0.789901) # T0473.t2k.bys.rdb (weight 0.748322) # T0473.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 T0473.t2k.str2.rdb # ============================================ # TARGET T0473 # 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 T0473.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 19.571 # # ============================================ # Comments from T0473.t2k.str4.rdb # ============================================ # TARGET T0473 # 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 T0473.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 19.571 # # ============================================ # Comments from T0473.t2k.pb.rdb # ============================================ # TARGET T0473 # 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 T0473.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 19.571 # # ============================================ # Comments from T0473.t2k.bys.rdb # ============================================ # TARGET T0473 # 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 T0473.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 19.571 # # ============================================ # Comments from T0473.t2k.alpha.rdb # ============================================ # TARGET T0473 # 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 T0473.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 19.571 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.4512 0.0496 0.4992 2 K 0.4487 0.0291 0.5222 3 I 0.4510 0.0357 0.5133 4 T 0.2318 0.0292 0.7390 5 K 0.0805 0.4393 0.4802 6 D 0.0777 0.3790 0.5433 7 M 0.2442 0.2456 0.5103 8 I 0.2309 0.3228 0.4463 9 I 0.0799 0.6887 0.2314 10 A 0.0311 0.8255 0.1434 11 D 0.0249 0.8724 0.1027 12 V 0.0285 0.8517 0.1198 13 L 0.0383 0.8067 0.1550 14 Q 0.0496 0.6929 0.2576 15 M 0.0808 0.5140 0.4052 16 D 0.1458 0.1789 0.6753 17 R 0.0240 0.5751 0.4009 18 G 0.0252 0.5024 0.4723 19 T 0.0551 0.6212 0.3237 20 A 0.0504 0.7459 0.2038 21 P 0.0403 0.8450 0.1147 22 I 0.0461 0.8542 0.0997 23 F 0.0330 0.8643 0.1027 24 I 0.0387 0.8190 0.1423 25 N 0.0464 0.6959 0.2577 26 N 0.0633 0.2385 0.6983 27 G 0.0588 0.0974 0.8439 28 M 0.1893 0.1143 0.6964 29 H 0.2633 0.1244 0.6123 30 C 0.2817 0.1652 0.5531 31 L 0.2269 0.1855 0.5876 32 G 0.1909 0.1106 0.6985 33 C 0.2251 0.0886 0.6864 34 P 0.1419 0.3127 0.5454 35 S 0.1179 0.3650 0.5171 36 S 0.1447 0.3222 0.5331 37 M 0.1025 0.3052 0.5923 38 G 0.0874 0.3533 0.5593 39 E 0.1413 0.4498 0.4089 40 S 0.1542 0.4363 0.4095 41 I 0.0180 0.7518 0.2302 42 E 0.0101 0.8670 0.1229 43 D 0.0114 0.9037 0.0849 44 A 0.0172 0.8958 0.0870 45 C 0.0190 0.8894 0.0916 46 A 0.0199 0.8581 0.1219 47 V 0.0264 0.7400 0.2336 48 H 0.0653 0.2917 0.6430 49 G 0.0543 0.1136 0.8322 50 I 0.1686 0.0838 0.7476 51 D 0.1663 0.0476 0.7860 52 A 0.0127 0.7415 0.2458 53 D 0.0092 0.8715 0.1193 54 K 0.0084 0.9205 0.0710 55 L 0.0085 0.9228 0.0687 56 V 0.0083 0.9233 0.0684 57 K 0.0083 0.9222 0.0695 58 E 0.0084 0.9104 0.0811 59 L 0.0090 0.9005 0.0905 60 N 0.0086 0.9024 0.0890 61 E 0.0086 0.9041 0.0873 62 Y 0.0107 0.8782 0.1111 63 F 0.0203 0.8484 0.1314 64 E 0.0226 0.7930 0.1844 65 K 0.0460 0.6601 0.2939 66 K 0.0810 0.5078 0.4112 67 E 0.1393 0.2966 0.5641 68 V 0.1832 0.1894 0.6274