# This file is the result of combining several RDB files, specifically # TR435.t04.str2.rdb (weight 1.54425) # TR435.t04.str4.rdb (weight 0.924988) # TR435.t04.pb.rdb (weight 0.789901) # TR435.t04.bys.rdb (weight 0.748322) # TR435.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 TR435.t04.str2.rdb # ============================================ # TARGET TR435 # 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 TR435.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 999 # # ============================================ # Comments from TR435.t04.str4.rdb # ============================================ # TARGET TR435 # 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 TR435.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 999 # # ============================================ # Comments from TR435.t04.pb.rdb # ============================================ # TARGET TR435 # 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 TR435.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 999 # # ============================================ # Comments from TR435.t04.bys.rdb # ============================================ # TARGET TR435 # 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 TR435.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 999 # # ============================================ # Comments from TR435.t04.alpha.rdb # ============================================ # TARGET TR435 # 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 TR435.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 999 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 A 0.2925 0.1639 0.5437 2 R 0.2740 0.1774 0.5485 3 L 0.2740 0.2044 0.5215 4 S 0.2413 0.1129 0.6458 5 L 0.2649 0.0404 0.6946 6 P 0.2380 0.0408 0.7212 7 K 0.3003 0.1438 0.5559 8 Q 0.4287 0.0873 0.4840 9 L 0.6593 0.0203 0.3204 10 V 0.7282 0.0127 0.2591 11 L 0.7239 0.0115 0.2646 12 R 0.6130 0.0301 0.3569 13 Q 0.5026 0.0634 0.4341 14 S 0.3957 0.0928 0.5114 15 I 0.3291 0.1652 0.5057 16 V 0.2213 0.1838 0.5949 17 G 0.1615 0.1156 0.7228 18 A 0.2041 0.1543 0.6416 19 E 0.2632 0.1093 0.6275 20 V 0.4904 0.0681 0.4415 21 G 0.6126 0.0430 0.3443 22 V 0.7319 0.0378 0.2304 23 W 0.7121 0.0367 0.2511 24 T 0.6229 0.0487 0.3285 25 G 0.4512 0.0976 0.4512 26 E 0.4901 0.0814 0.4285 27 T 0.4795 0.0614 0.4591 28 I 0.3722 0.0272 0.6006 29 P 0.2105 0.0390 0.7505 30 V 0.1341 0.2635 0.6024 31 R 0.0900 0.1589 0.7511 32 T 0.3673 0.0551 0.5777 33 C 0.6043 0.0407 0.3550 34 F 0.6563 0.0376 0.3061 35 G 0.6174 0.0236 0.3590 36 P 0.5750 0.0901 0.3349 37 L 0.5334 0.0922 0.3744 38 I 0.4252 0.0951 0.4797 39 G 0.3495 0.0779 0.5725 40 Q 0.5321 0.0750 0.3929 41 Q 0.5909 0.0498 0.3593 42 S 0.4630 0.0675 0.4696 43 H 0.2795 0.0748 0.6457 44 S 0.1173 0.4661 0.4166 45 M 0.0583 0.6851 0.2566 46 E 0.0797 0.7231 0.1972 47 V 0.0675 0.7622 0.1703 48 A 0.0468 0.7928 0.1604 49 E 0.0542 0.7437 0.2021 50 W 0.0836 0.6329 0.2835 51 T 0.1054 0.5294 0.3652 52 D 0.0979 0.5242 0.3780 53 K 0.0881 0.5001 0.4118 54 A 0.1129 0.4260 0.4610 55 V 0.0904 0.4619 0.4477 56 N 0.1100 0.3542 0.5358 57 H 0.2117 0.3211 0.4672 58 I 0.3417 0.2508 0.4074 59 W 0.4546 0.2093 0.3362 60 K 0.5831 0.1543 0.2627 61 I 0.6179 0.1236 0.2585 62 Y 0.5476 0.1175 0.3348 63 H 0.3573 0.1601 0.4826 64 N 0.1847 0.1350 0.6803 65 G 0.1371 0.1006 0.7624 66 V 0.2491 0.0733 0.6776 67 L 0.3202 0.1012 0.5787 68 E 0.4078 0.1030 0.4892 69 F 0.6584 0.0364 0.3052 70 C 0.7302 0.0174 0.2524 71 I 0.7476 0.0159 0.2365 72 I 0.6196 0.0301 0.3502 73 T 0.3865 0.0962 0.5173 74 T 0.2442 0.1099 0.6459 75 D 0.1661 0.2450 0.5889 76 E 0.0767 0.4094 0.5139 77 N 0.0978 0.3172 0.5850 78 E 0.1212 0.3050 0.5739 79 C 0.1396 0.3519 0.5085 80 N 0.1425 0.4425 0.4150 81 W 0.0944 0.6515 0.2541 82 M 0.0983 0.7360 0.1657 83 M 0.1197 0.7400 0.1402 84 F 0.1461 0.6840 0.1699 85 V 0.1764 0.6217 0.2019 86 R 0.1391 0.5320 0.3288 87 K 0.1101 0.4252 0.4647 88 A 0.1285 0.3113 0.5601 89 R 0.1522 0.2153 0.6324 90 N 0.1788 0.0801 0.7411 91 R 0.0438 0.4404 0.5158 92 E 0.0696 0.3446 0.5858 93 E 0.1888 0.3722 0.4390 94 Q 0.3318 0.2468 0.4214 95 N 0.4945 0.1239 0.3816 96 L 0.6280 0.0605 0.3115 97 V 0.7273 0.0303 0.2424 98 A 0.7138 0.0210 0.2652 99 Y 0.6139 0.0162 0.3699 100 P 0.4387 0.0893 0.4720 101 H 0.1786 0.1581 0.6633 102 D 0.1187 0.1038 0.7774 103 G 0.1848 0.0588 0.7565 104 K 0.5615 0.0158 0.4227 105 I 0.7653 0.0062 0.2285 106 F 0.8166 0.0057 0.1777 107 F 0.8250 0.0042 0.1708 108 C 0.8108 0.0073 0.1819 109 T 0.7539 0.0117 0.2345 110 S 0.5998 0.0587 0.3415 111 Q 0.4797 0.0890 0.4312 112 D 0.4106 0.0584 0.5310 113 I 0.3400 0.0276 0.6324 114 P 0.1882 0.0185 0.7933 115 P 0.0920 0.2637 0.6442 116 E 0.0438 0.1696 0.7865 117 N 0.2799 0.1538 0.5663 118 E 0.5879 0.0576 0.3546 119 L 0.7464 0.0282 0.2254 120 L 0.7667 0.0263 0.2071 121 F 0.7570 0.0244 0.2186 122 Y 0.5618 0.0795 0.3587 123 Y 0.3788 0.1582 0.4630 124 S 0.2355 0.1811 0.5834 125 R 0.1139 0.4168 0.4693 126 D 0.1104 0.5064 0.3832 127 Y 0.0642 0.6866 0.2492 128 A 0.0412 0.7483 0.2105 129 Q 0.0383 0.7509 0.2108 130 Q 0.0690 0.5965 0.3344 131 I 0.1135 0.2617 0.6248 132 G 0.0890 0.1055 0.8055 133 V 0.1895 0.0250 0.7854 134 P 0.1744 0.0579 0.7676 135 E 0.1759 0.1806 0.6435