# This file is the result of combining several RDB files, specifically # T0407.t04.str2.rdb (weight 1.54425) # T0407.t04.str4.rdb (weight 0.924988) # T0407.t04.pb.rdb (weight 0.789901) # T0407.t04.bys.rdb (weight 0.748322) # T0407.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 T0407.t04.str2.rdb # ============================================ # TARGET T0407 # 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 T0407.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 # # ============================================ # Comments from T0407.t04.str4.rdb # ============================================ # TARGET T0407 # 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 T0407.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 # # ============================================ # Comments from T0407.t04.pb.rdb # ============================================ # TARGET T0407 # 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 T0407.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 # # ============================================ # Comments from T0407.t04.bys.rdb # ============================================ # TARGET T0407 # 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 T0407.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 # # ============================================ # Comments from T0407.t04.alpha.rdb # ============================================ # TARGET T0407 # 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 T0407.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 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 A 0.3012 0.2793 0.4195 2 A 0.3458 0.3411 0.3131 3 Y 0.4562 0.2920 0.2518 4 F 0.3417 0.4054 0.2529 5 H 0.2719 0.5080 0.2202 6 E 0.3131 0.4864 0.2005 7 L 0.3071 0.4602 0.2327 8 L 0.3329 0.3505 0.3166 9 I 0.2617 0.2935 0.4448 10 G 0.1710 0.2044 0.6245 11 R 0.0855 0.4898 0.4247 12 E 0.0307 0.6940 0.2753 13 D 0.0274 0.7400 0.2326 14 L 0.0342 0.6804 0.2853 15 L 0.0469 0.6543 0.2988 16 R 0.0595 0.6283 0.3122 17 P 0.0259 0.7594 0.2147 18 F 0.0289 0.7604 0.2107 19 F 0.0361 0.7627 0.2012 20 E 0.0469 0.7010 0.2520 21 K 0.0855 0.5483 0.3663 22 C 0.2356 0.2719 0.4925 23 V 0.3265 0.1541 0.5194 24 K 0.3602 0.1073 0.5325 25 I 0.2848 0.3141 0.4011 26 E 0.2499 0.3721 0.3781 27 E 0.4265 0.2405 0.3330 28 V 0.4243 0.1605 0.4153 29 S 0.3477 0.1477 0.5046 30 R 0.2671 0.2554 0.4775 31 N 0.2170 0.1847 0.5983 32 E 0.1946 0.2717 0.5337 33 Q 0.1912 0.1695 0.6393 34 G 0.2587 0.0835 0.6577 35 V 0.5049 0.0241 0.4711 36 T 0.6807 0.0163 0.3030 37 L 0.7544 0.0175 0.2281 38 S 0.7334 0.0197 0.2469 39 I 0.6346 0.0522 0.3132 40 T 0.4686 0.0859 0.4455 41 N 0.3279 0.0935 0.5786 42 V 0.1732 0.3566 0.4702 43 T 0.1398 0.4879 0.3723 44 D 0.1895 0.5726 0.2380 45 L 0.2513 0.5614 0.1873 46 V 0.2989 0.5585 0.1426 47 L 0.3881 0.4671 0.1448 48 K 0.3770 0.4338 0.1892 49 L 0.2864 0.4649 0.2487 50 K 0.2031 0.4740 0.3229 51 K 0.1788 0.4413 0.3799 52 T 0.1871 0.3192 0.4937 53 A 0.1546 0.3181 0.5273 54 H 0.1670 0.2504 0.5826 55 D 0.2137 0.2132 0.5730 56 T 0.2357 0.2980 0.4663 57 L 0.3965 0.2829 0.3206 58 L 0.6507 0.1262 0.2230 59 V 0.7369 0.0710 0.1921 60 Y 0.7357 0.0502 0.2140 61 F 0.6440 0.1181 0.2379 62 R 0.5389 0.1935 0.2677 63 D 0.4809 0.1478 0.3713 64 M 0.4894 0.1033 0.4073 65 T 0.4975 0.0754 0.4271 66 L 0.4569 0.0667 0.4764 67 K 0.3739 0.0398 0.5863 68 P 0.3230 0.1262 0.5508 69 H 0.2637 0.1308 0.6055 70 T 0.3652 0.0871 0.5477 71 R 0.4820 0.0642 0.4538 72 Y 0.6747 0.0306 0.2947 73 T 0.7405 0.0124 0.2471 74 V 0.7798 0.0113 0.2089 75 R 0.7656 0.0113 0.2231 76 I 0.7431 0.0242 0.2326 77 G 0.6246 0.0457 0.3297 78 F 0.4444 0.1320 0.4236 79 K 0.2883 0.2350 0.4766 80 Q 0.1802 0.1902 0.6296 81 G 0.1676 0.1150 0.7173 82 I 0.2895 0.0973 0.6132 83 K 0.2659 0.1003 0.6339 84 G 0.1970 0.1166 0.6864 85 G 0.1796 0.1135 0.7069 86 D 0.3004 0.0903 0.6093 87 V 0.4360 0.0960 0.4680 88 N 0.4371 0.0860 0.4769 89 F 0.5650 0.0599 0.3752 90 E 0.6162 0.0552 0.3287 91 V 0.6066 0.0489 0.3445 92 T 0.5100 0.0769 0.4131 93 N 0.5259 0.0591 0.4150 94 F 0.6664 0.0281 0.3055 95 I 0.6932 0.0269 0.2800 96 V 0.6836 0.0232 0.2932 97 A 0.4575 0.0249 0.5176 98 P 0.2746 0.1058 0.6196 99 D 0.1940 0.1600 0.6460 100 K 0.1074 0.2216 0.6709 101 G 0.1077 0.1150 0.7773 102 L 0.3380 0.0577 0.6043 103 K 0.4933 0.0472 0.4595 104 Y 0.6872 0.0251 0.2877 105 T 0.7264 0.0143 0.2593 106 I 0.7473 0.0123 0.2404 107 S 0.6527 0.0168 0.3304 108 L 0.4275 0.0584 0.5141