# This file is the result of combining several RDB files, specifically # T0429.t06.str2.rdb (weight 1.54425) # T0429.t06.str4.rdb (weight 0.924988) # T0429.t06.pb.rdb (weight 0.789901) # T0429.t06.bys.rdb (weight 0.748322) # T0429.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 T0429.t06.str2.rdb # ============================================ # TARGET T0429 # 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 T0429.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 6.4855 # # ============================================ # Comments from T0429.t06.str4.rdb # ============================================ # TARGET T0429 # 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 T0429.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 6.4855 # # ============================================ # Comments from T0429.t06.pb.rdb # ============================================ # TARGET T0429 # 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 T0429.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 6.4855 # # ============================================ # Comments from T0429.t06.bys.rdb # ============================================ # TARGET T0429 # 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 T0429.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 6.4855 # # ============================================ # Comments from T0429.t06.alpha.rdb # ============================================ # TARGET T0429 # 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 T0429.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 6.4855 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 R 0.2070 0.1127 0.6803 2 K 0.2188 0.0817 0.6995 3 A 0.2523 0.0492 0.6985 4 P 0.2167 0.1244 0.6589 5 S 0.2134 0.1679 0.6187 6 R 0.1732 0.1988 0.6281 7 D 0.1951 0.1127 0.6922 8 E 0.2852 0.0476 0.6672 9 P 0.2858 0.0716 0.6427 10 C 0.2814 0.0904 0.6283 11 S 0.2244 0.1240 0.6516 12 S 0.1778 0.1799 0.6423 13 T 0.1797 0.1739 0.6464 14 S 0.2059 0.1185 0.6756 15 R 0.2554 0.0619 0.6828 16 P 0.2290 0.1083 0.6627 17 A 0.2569 0.1122 0.6309 18 L 0.2184 0.1336 0.6479 19 E 0.1559 0.2831 0.5610 20 E 0.2041 0.2738 0.5221 21 D 0.3984 0.1104 0.4912 22 V 0.6940 0.0274 0.2786 23 I 0.7481 0.0162 0.2358 24 Y 0.8114 0.0079 0.1807 25 H 0.8058 0.0064 0.1878 26 V 0.8045 0.0063 0.1892 27 K 0.7566 0.0110 0.2325 28 Y 0.6000 0.0416 0.3584 29 D 0.3179 0.1414 0.5407 30 D 0.2077 0.1406 0.6516 31 Y 0.2747 0.0551 0.6702 32 P 0.1372 0.2546 0.6082 33 E 0.0698 0.3455 0.5847 34 N 0.0911 0.1786 0.7303 35 G 0.1984 0.0879 0.7138 36 V 0.5438 0.0293 0.4269 37 V 0.6927 0.0237 0.2836 38 Q 0.7194 0.0189 0.2617 39 M 0.6678 0.0209 0.3113 40 N 0.4368 0.0327 0.5305 41 S 0.2508 0.2097 0.5395 42 R 0.1464 0.3399 0.5136 43 D 0.1787 0.2317 0.5895 44 V 0.2827 0.1485 0.5688 45 R 0.2717 0.1260 0.6023 46 A 0.1488 0.4732 0.3780 47 R 0.0847 0.6287 0.2866 48 A 0.1420 0.6104 0.2477 49 R 0.1828 0.5512 0.2659 50 T 0.2407 0.5003 0.2589 51 I 0.3125 0.3397 0.3478 52 I 0.4000 0.1949 0.4051 53 K 0.3017 0.1400 0.5583 54 W 0.1498 0.3817 0.4685 55 Q 0.1053 0.4198 0.4749 56 D 0.1437 0.3059 0.5505 57 L 0.3075 0.1143 0.5781 58 E 0.3127 0.0764 0.6108 59 V 0.2703 0.1427 0.5869 60 G 0.2528 0.0926 0.6546 61 Q 0.5350 0.0444 0.4206 62 V 0.7465 0.0126 0.2408 63 V 0.7811 0.0132 0.2057 64 M 0.7932 0.0101 0.1967 65 L 0.7475 0.0209 0.2315 66 N 0.5901 0.0355 0.3744 67 Y 0.4375 0.0483 0.5142 68 N 0.2534 0.0267 0.7199 69 P 0.0498 0.3916 0.5586 70 D 0.0549 0.3128 0.6323 71 N 0.1302 0.2076 0.6621 72 P 0.0883 0.3888 0.5229 73 K 0.0845 0.4164 0.4991 74 E 0.1217 0.3395 0.5388 75 R 0.2022 0.1561 0.6416 76 G 0.3006 0.0862 0.6132 77 F 0.5829 0.0450 0.3721 78 W 0.7027 0.0450 0.2524 79 Y 0.6700 0.0735 0.2565 80 D 0.6145 0.0934 0.2920 81 A 0.6041 0.1796 0.2163 82 E 0.6233 0.1644 0.2124 83 I 0.6060 0.1680 0.2260 84 S 0.4838 0.2324 0.2838 85 R 0.4234 0.2201 0.3564 86 K 0.3547 0.2543 0.3910 87 R 0.3019 0.2593 0.4388 88 E 0.2596 0.2126 0.5278 89 T 0.2608 0.1610 0.5782 90 R 0.2360 0.1383 0.6257