# This file is the result of combining several RDB files, specifically # TR488.t04.str2.rdb (weight 1.54425) # TR488.t04.str4.rdb (weight 0.924988) # TR488.t04.pb.rdb (weight 0.789901) # TR488.t04.bys.rdb (weight 0.748322) # TR488.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 TR488.t04.str2.rdb # ============================================ # TARGET TR488 # 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 TR488.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 1830 # # ============================================ # Comments from TR488.t04.str4.rdb # ============================================ # TARGET TR488 # 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 TR488.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 1830 # # ============================================ # Comments from TR488.t04.pb.rdb # ============================================ # TARGET TR488 # 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 TR488.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 1830 # # ============================================ # Comments from TR488.t04.bys.rdb # ============================================ # TARGET TR488 # 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 TR488.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 1830 # # ============================================ # Comments from TR488.t04.alpha.rdb # ============================================ # TARGET TR488 # 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 TR488.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 1830 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 S 0.2511 0.0673 0.6817 2 M 0.3497 0.0588 0.5915 3 E 0.5364 0.0384 0.4252 4 I 0.6750 0.0120 0.3130 5 L 0.7152 0.0162 0.2686 6 Q 0.7923 0.0048 0.2028 7 V 0.8141 0.0051 0.1807 8 A 0.8089 0.0051 0.1861 9 L 0.7943 0.0052 0.2004 10 H 0.7527 0.0124 0.2349 11 K 0.6627 0.0240 0.3133 12 R 0.4107 0.0488 0.5405 13 D 0.2042 0.1559 0.6399 14 S 0.1306 0.1631 0.7062 15 G 0.1293 0.1092 0.7615 16 E 0.2914 0.1031 0.6055 17 Q 0.4331 0.0784 0.4885 18 L 0.5352 0.0532 0.4116 19 G 0.6726 0.0222 0.3052 20 I 0.7724 0.0073 0.2203 21 K 0.7786 0.0076 0.2137 22 L 0.7553 0.0083 0.2364 23 V 0.6559 0.0355 0.3086 24 R 0.4476 0.0478 0.5047 25 R 0.2857 0.0958 0.6184 26 T 0.2051 0.1458 0.6491 27 D 0.1699 0.1115 0.7186 28 E 0.2157 0.0686 0.7156 29 P 0.2217 0.1153 0.6630 30 G 0.3512 0.0526 0.5962 31 V 0.6875 0.0137 0.2988 32 F 0.7370 0.0126 0.2505 33 I 0.7056 0.0233 0.2711 34 L 0.6403 0.0734 0.2863 35 D 0.6978 0.0431 0.2591 36 L 0.5318 0.0942 0.3740 37 L 0.3933 0.0805 0.5261 38 E 0.1508 0.2346 0.6147 39 G 0.0950 0.1442 0.7608 40 G 0.1725 0.1322 0.6953 41 L 0.1713 0.4097 0.4190 42 A 0.1791 0.5020 0.3189 43 A 0.1966 0.4673 0.3360 44 Q 0.1595 0.4289 0.4116 45 D 0.1150 0.1849 0.7001 46 G 0.1255 0.0831 0.7914 47 R 0.3502 0.0363 0.6135 48 L 0.4371 0.0353 0.5276 49 S 0.3168 0.0222 0.6610 50 S 0.1333 0.2191 0.6476 51 N 0.0577 0.1432 0.7990 52 D 0.3409 0.0600 0.5991 53 R 0.6232 0.0632 0.3136 54 V 0.7504 0.0341 0.2155 55 L 0.7907 0.0170 0.1924 56 A 0.7852 0.0119 0.2029 57 I 0.7027 0.0375 0.2598 58 N 0.3926 0.0450 0.5624 59 G 0.1933 0.0611 0.7456 60 H 0.4551 0.0416 0.5032 61 D 0.4956 0.0392 0.4651 62 L 0.2921 0.2229 0.4850 63 K 0.1684 0.2837 0.5479 64 Y 0.1416 0.1625 0.6959 65 G 0.1638 0.1008 0.7354 66 T 0.1709 0.0302 0.7989 67 P 0.0134 0.7252 0.2614 68 E 0.0093 0.8685 0.1223 69 L 0.0084 0.9207 0.0709 70 A 0.0083 0.9238 0.0679 71 A 0.0083 0.9240 0.0677 72 Q 0.0083 0.9246 0.0671 73 I 0.0083 0.9237 0.0680 74 I 0.0086 0.9173 0.0741 75 Q 0.0099 0.8857 0.1044 76 A 0.0175 0.7307 0.2518 77 S 0.0691 0.2341 0.6969 78 G 0.0646 0.0894 0.8460 79 E 0.2007 0.0637 0.7355 80 R 0.4828 0.0264 0.4908 81 V 0.7026 0.0117 0.2857 82 N 0.7744 0.0067 0.2188 83 L 0.8094 0.0048 0.1859 84 T 0.8040 0.0057 0.1903 85 I 0.7752 0.0063 0.2185 86 A 0.6565 0.0176 0.3259 87 R 0.4043 0.0180 0.5777 88 P 0.2077 0.0860 0.7063 89 G 0.1574 0.0850 0.7576 90 K 0.2062 0.0364 0.7575 91 P 0.2232 0.1107 0.6661 92 E 0.2717 0.1632 0.5650 93 I 0.2846 0.1641 0.5513 94 E 0.2450 0.1486 0.6064 95 L 0.2188 0.1812 0.6001