# This file is the result of combining several RDB files, specifically # T0404.t04.str2.rdb (weight 1.54425) # T0404.t04.str4.rdb (weight 0.924988) # T0404.t04.pb.rdb (weight 0.789901) # T0404.t04.bys.rdb (weight 0.748322) # T0404.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 T0404.t04.str2.rdb # ============================================ # TARGET T0404 # 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 T0404.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 82.5178 # # ============================================ # Comments from T0404.t04.str4.rdb # ============================================ # TARGET T0404 # 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 T0404.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 82.5178 # # ============================================ # Comments from T0404.t04.pb.rdb # ============================================ # TARGET T0404 # 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 T0404.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 82.5178 # # ============================================ # Comments from T0404.t04.bys.rdb # ============================================ # TARGET T0404 # 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 T0404.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 82.5178 # # ============================================ # Comments from T0404.t04.alpha.rdb # ============================================ # TARGET T0404 # 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 T0404.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 82.5178 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.2177 0.1965 0.5859 2 S 0.1840 0.1923 0.6237 3 K 0.1259 0.3638 0.5103 4 R 0.1387 0.2957 0.5655 5 A 0.2319 0.2341 0.5340 6 N 0.3833 0.1208 0.4959 7 K 0.6458 0.0425 0.3117 8 L 0.7320 0.0167 0.2512 9 V 0.7912 0.0151 0.1937 10 I 0.8073 0.0079 0.1848 11 V 0.7739 0.0225 0.2036 12 T 0.6696 0.0310 0.2994 13 E 0.3457 0.0683 0.5860 14 K 0.1007 0.4706 0.4287 15 V 0.0417 0.6812 0.2771 16 L 0.0343 0.7727 0.1930 17 L 0.0100 0.8783 0.1117 18 K 0.0084 0.9168 0.0748 19 K 0.0083 0.9211 0.0705 20 V 0.0083 0.9221 0.0696 21 A 0.0083 0.9235 0.0682 22 K 0.0083 0.9245 0.0673 23 I 0.0083 0.9228 0.0689 24 I 0.0084 0.9160 0.0756 25 E 0.0087 0.9007 0.0905 26 E 0.0122 0.8133 0.1745 27 A 0.0597 0.2996 0.6407 28 G 0.0524 0.0799 0.8677 29 A 0.1671 0.0629 0.7699 30 T 0.2340 0.0928 0.6731 31 G 0.4407 0.0539 0.5055 32 Y 0.6387 0.0205 0.3408 33 T 0.7108 0.0146 0.2745 34 V 0.7006 0.0240 0.2754 35 V 0.6237 0.0362 0.3401 36 D 0.5301 0.0505 0.4194 37 T 0.4012 0.1020 0.4968 38 G 0.2741 0.1044 0.6215 39 G 0.2167 0.0977 0.6856 40 K 0.2386 0.1224 0.6390 41 G 0.2305 0.0887 0.6809 42 S 0.2218 0.1545 0.6236 43 R 0.1851 0.1637 0.6512 44 N 0.2002 0.1345 0.6653 45 V 0.3730 0.1089 0.5181 46 R 0.4425 0.1086 0.4490 47 S 0.4155 0.1330 0.4515 48 T 0.2760 0.1185 0.6055 49 G 0.1762 0.0683 0.7555 50 K 0.2378 0.0415 0.7207 51 P 0.2562 0.1390 0.6048 52 N 0.3121 0.1405 0.5474 53 T 0.3410 0.1211 0.5379 54 S 0.3119 0.1381 0.5500 55 D 0.2565 0.1331 0.6104 56 T 0.2184 0.1578 0.6238 57 D 0.2716 0.0934 0.6350 58 S 0.1642 0.2619 0.5739 59 N 0.2534 0.0990 0.6475 60 V 0.6030 0.0111 0.3859 61 K 0.7240 0.0111 0.2649 62 F 0.8161 0.0044 0.1795 63 E 0.8094 0.0057 0.1849 64 V 0.8077 0.0047 0.1875 65 L 0.7868 0.0075 0.2057 66 T 0.6879 0.0103 0.3018 67 E 0.3417 0.0289 0.6295 68 N 0.1740 0.0839 0.7422 69 R 0.0225 0.6490 0.3285 70 E 0.0129 0.8202 0.1669 71 M 0.0118 0.8824 0.1058 72 A 0.0084 0.9124 0.0792 73 E 0.0083 0.9210 0.0707 74 K 0.0083 0.9226 0.0691 75 I 0.0083 0.9227 0.0690 76 A 0.0083 0.9230 0.0687 77 D 0.0083 0.9243 0.0674 78 Q 0.0083 0.9241 0.0676 79 V 0.0083 0.9209 0.0707 80 A 0.0084 0.9169 0.0747 81 I 0.0091 0.9058 0.0851 82 K 0.0156 0.8436 0.1408 83 F 0.0522 0.6434 0.3044 84 F 0.1114 0.3895 0.4991 85 T 0.1651 0.1727 0.6622 86 D 0.1252 0.1402 0.7346 87 Y 0.1859 0.1672 0.6468 88 A 0.1893 0.1120 0.6987 89 G 0.3212 0.0445 0.6343 90 I 0.6735 0.0096 0.3169 91 I 0.7642 0.0062 0.2296 92 Y 0.8017 0.0067 0.1916 93 I 0.7976 0.0060 0.1964 94 C 0.6999 0.0094 0.2907 95 E 0.6218 0.0169 0.3613 96 A 0.5556 0.0289 0.4155 97 E 0.5997 0.0377 0.3626 98 V 0.7263 0.0155 0.2582 99 L 0.7196 0.0173 0.2631 100 Y 0.7485 0.0108 0.2407 101 G 0.6453 0.0297 0.3250 102 R 0.5602 0.0545 0.3853 103 T 0.4667 0.0543 0.4790 104 F 0.3304 0.0919 0.5777 105 C 0.3293 0.0852 0.5855 106 G 0.2280 0.0445 0.7276 107 P 0.1429 0.1880 0.6691 108 D 0.1021 0.2546 0.6434 109 G 0.0978 0.1784 0.7237 110 C 0.2130 0.1315 0.6555