# This file is the result of combining several RDB files, specifically # T0429.t04.str2.rdb (weight 1.54425) # T0429.t04.str4.rdb (weight 0.924988) # T0429.t04.pb.rdb (weight 0.789901) # T0429.t04.bys.rdb (weight 0.748322) # T0429.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 T0429.t04.str2.rdb # ============================================ # TARGET T0429 # 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 T0429.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 6.48049 # # ============================================ # Comments from T0429.t04.str4.rdb # ============================================ # TARGET T0429 # 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 T0429.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 6.48049 # # ============================================ # Comments from T0429.t04.pb.rdb # ============================================ # TARGET T0429 # 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 T0429.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 6.48049 # # ============================================ # Comments from T0429.t04.bys.rdb # ============================================ # TARGET T0429 # 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 T0429.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 6.48049 # # ============================================ # Comments from T0429.t04.alpha.rdb # ============================================ # TARGET T0429 # 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 T0429.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 6.48049 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 R 0.1952 0.1484 0.6563 2 K 0.2194 0.1056 0.6750 3 A 0.2654 0.0527 0.6820 4 P 0.2234 0.1124 0.6642 5 S 0.2286 0.1513 0.6201 6 R 0.2104 0.1804 0.6091 7 D 0.2023 0.1135 0.6842 8 E 0.2700 0.0504 0.6796 9 P 0.2579 0.0946 0.6476 10 C 0.2983 0.1238 0.5778 11 S 0.2828 0.1369 0.5803 12 S 0.2692 0.1853 0.5456 13 T 0.2290 0.1699 0.6011 14 S 0.2154 0.1254 0.6592 15 R 0.2705 0.0597 0.6698 16 P 0.2388 0.1158 0.6454 17 A 0.2416 0.1593 0.5991 18 L 0.2169 0.1789 0.6042 19 E 0.1995 0.2343 0.5662 20 E 0.2042 0.2662 0.5295 21 D 0.3637 0.1290 0.5073 22 V 0.6376 0.0295 0.3328 23 I 0.7301 0.0173 0.2526 24 Y 0.7976 0.0085 0.1939 25 H 0.8101 0.0061 0.1838 26 V 0.8063 0.0060 0.1876 27 K 0.7289 0.0104 0.2607 28 Y 0.5925 0.0407 0.3668 29 D 0.2879 0.1742 0.5379 30 D 0.1780 0.1539 0.6681 31 Y 0.2683 0.0508 0.6809 32 P 0.1514 0.2173 0.6313 33 E 0.0907 0.3439 0.5654 34 N 0.1291 0.1581 0.7129 35 G 0.2648 0.0734 0.6617 36 V 0.5829 0.0324 0.3847 37 V 0.7099 0.0232 0.2669 38 Q 0.7460 0.0130 0.2410 39 M 0.7008 0.0241 0.2751 40 N 0.4674 0.0338 0.4988 41 S 0.2271 0.2761 0.4968 42 R 0.1361 0.3454 0.5185 43 D 0.2125 0.2010 0.5866 44 V 0.2910 0.1106 0.5984 45 R 0.2463 0.1045 0.6492 46 A 0.1617 0.4718 0.3665 47 R 0.1434 0.5039 0.3527 48 A 0.1615 0.5784 0.2601 49 R 0.2365 0.4821 0.2814 50 T 0.4522 0.2876 0.2602 51 I 0.5010 0.1791 0.3198 52 I 0.4837 0.1092 0.4071 53 K 0.3294 0.0851 0.5855 54 W 0.1713 0.3670 0.4617 55 Q 0.1337 0.3928 0.4735 56 D 0.2307 0.2463 0.5230 57 L 0.4059 0.0661 0.5281 58 E 0.3816 0.0662 0.5522 59 V 0.3161 0.1018 0.5821 60 G 0.2744 0.0749 0.6507 61 Q 0.5429 0.0257 0.4315 62 V 0.7435 0.0080 0.2485 63 V 0.7769 0.0107 0.2124 64 M 0.7803 0.0096 0.2101 65 L 0.7525 0.0213 0.2263 66 N 0.6159 0.0232 0.3609 67 Y 0.3482 0.0625 0.5893 68 N 0.2314 0.0252 0.7434 69 P 0.0396 0.3929 0.5675 70 D 0.0725 0.2574 0.6701 71 N 0.2034 0.1063 0.6903 72 P 0.1359 0.2690 0.5951 73 K 0.1126 0.3949 0.4925 74 E 0.1687 0.2514 0.5799 75 R 0.2074 0.1378 0.6548 76 G 0.2404 0.0833 0.6763 77 F 0.4832 0.0670 0.4498 78 W 0.6210 0.0642 0.3148 79 Y 0.6600 0.0686 0.2714 80 D 0.6155 0.0908 0.2936 81 A 0.5686 0.1620 0.2694 82 E 0.5636 0.2208 0.2156 83 I 0.4886 0.2594 0.2520 84 S 0.3679 0.3363 0.2958 85 R 0.3236 0.3623 0.3141 86 K 0.2434 0.3874 0.3692 87 R 0.2053 0.3771 0.4176 88 E 0.2337 0.2729 0.4935 89 T 0.2288 0.1831 0.5880 90 R 0.2233 0.1388 0.6380