# This file is the result of combining several RDB files, specifically # T0464.t06.str2.rdb (weight 1.54425) # T0464.t06.str4.rdb (weight 0.924988) # T0464.t06.pb.rdb (weight 0.789901) # T0464.t06.bys.rdb (weight 0.748322) # T0464.t06.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 T0464.t06.str2.rdb # ============================================ # TARGET T0464 # 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 T0464.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 5.24702 # # ============================================ # Comments from T0464.t06.str4.rdb # ============================================ # TARGET T0464 # 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 T0464.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 5.24702 # # ============================================ # Comments from T0464.t06.pb.rdb # ============================================ # TARGET T0464 # 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 T0464.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 5.24702 # # ============================================ # Comments from T0464.t06.bys.rdb # ============================================ # TARGET T0464 # 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 T0464.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 5.24702 # # ============================================ # Comments from T0464.t06.alpha.rdb # ============================================ # TARGET T0464 # 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 T0464.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 5.24702 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.1923 0.1750 0.6328 2 D 0.1582 0.1429 0.6989 3 R 0.0196 0.7552 0.2252 4 K 0.0146 0.8381 0.1473 5 L 0.0233 0.8610 0.1158 6 L 0.0260 0.8625 0.1114 7 H 0.0274 0.8442 0.1284 8 L 0.0449 0.7737 0.1814 9 L 0.1085 0.5688 0.3228 10 C 0.2254 0.2416 0.5330 11 S 0.2078 0.0680 0.7242 12 P 0.0719 0.3301 0.5980 13 D 0.0561 0.3005 0.6434 14 T 0.1104 0.1923 0.6973 15 R 0.1133 0.1541 0.7326 16 Q 0.2498 0.0482 0.7020 17 P 0.2894 0.1066 0.6040 18 L 0.3573 0.1791 0.4635 19 S 0.3547 0.2539 0.3914 20 L 0.2289 0.5030 0.2681 21 L 0.1484 0.5830 0.2685 22 E 0.1047 0.6041 0.2913 23 S 0.0518 0.7042 0.2440 24 K 0.0240 0.7615 0.2144 25 G 0.0192 0.8250 0.1558 26 L 0.0102 0.8921 0.0977 27 E 0.0084 0.9152 0.0764 28 A 0.0084 0.9165 0.0751 29 L 0.0097 0.8982 0.0921 30 N 0.0093 0.8976 0.0931 31 K 0.0087 0.8982 0.0932 32 A 0.0105 0.8728 0.1168 33 I 0.0243 0.8191 0.1566 34 A 0.0300 0.6896 0.2805 35 S 0.0632 0.3365 0.6003 36 G 0.0817 0.1262 0.7921 37 T 0.2738 0.1420 0.5842 38 V 0.4636 0.1431 0.3933 39 Q 0.4095 0.2084 0.3822 40 R 0.3601 0.1826 0.4573 41 A 0.2384 0.2353 0.5262 42 D 0.1279 0.1207 0.7514 43 G 0.0764 0.0882 0.8354 44 S 0.2684 0.0615 0.6701 45 I 0.4847 0.0920 0.4232 46 Q 0.4092 0.1505 0.4403 47 N 0.4006 0.1348 0.4646 48 Q 0.4066 0.0867 0.5067 49 S 0.3100 0.1175 0.5725 50 L 0.1938 0.3300 0.4762 51 H 0.1328 0.4217 0.4455 52 E 0.2065 0.3902 0.4032 53 A 0.4114 0.2307 0.3579 54 L 0.5687 0.1346 0.2967 55 I 0.5826 0.0828 0.3346 56 T 0.4172 0.0842 0.4986 57 R 0.2100 0.1876 0.6024 58 D 0.1792 0.1591 0.6617 59 R 0.1257 0.3376 0.5367 60 K 0.2089 0.3066 0.4845 61 Q 0.4568 0.1540 0.3892 62 V 0.5992 0.0498 0.3510 63 F 0.6703 0.0325 0.2972 64 R 0.6749 0.0294 0.2956 65 I 0.5280 0.0839 0.3881 66 E 0.2808 0.1893 0.5299 67 D 0.1515 0.1686 0.6799 68 S 0.1519 0.1158 0.7324 69 I 0.3425 0.0336 0.6239 70 P 0.4382 0.0430 0.5187 71 V 0.6639 0.0487 0.2874 72 L 0.6122 0.0696 0.3181 73 L 0.4455 0.1238 0.4307 74 P 0.1868 0.3998 0.4133 75 E 0.0432 0.6847 0.2722 76 E 0.0318 0.7183 0.2499 77 A 0.0543 0.7007 0.2450 78 I 0.1015 0.6613 0.2372 79 A 0.0713 0.7099 0.2188 80 T 0.0656 0.7434 0.1910 81 I 0.0782 0.7017 0.2201 82 Q 0.1018 0.6410 0.2572 83 I 0.1385 0.5504 0.3111 84 A 0.1061 0.4281 0.4659 85 N 0.1116 0.2452 0.6432 86 F 0.1918 0.0829 0.7253 87 P 0.1260 0.2380 0.6360 88 D 0.1173 0.2433 0.6394 89 K 0.1228 0.2389 0.6382