# This file is the result of combining several RDB files, specifically # T0451.t04.str2.rdb (weight 1.54425) # T0451.t04.str4.rdb (weight 0.924988) # T0451.t04.pb.rdb (weight 0.789901) # T0451.t04.bys.rdb (weight 0.748322) # T0451.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 T0451.t04.str2.rdb # ============================================ # TARGET T0451 # 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 T0451.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 381 # # ============================================ # Comments from T0451.t04.str4.rdb # ============================================ # TARGET T0451 # 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 T0451.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 381 # # ============================================ # Comments from T0451.t04.pb.rdb # ============================================ # TARGET T0451 # 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 T0451.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 381 # # ============================================ # Comments from T0451.t04.bys.rdb # ============================================ # TARGET T0451 # 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 T0451.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 381 # # ============================================ # Comments from T0451.t04.alpha.rdb # ============================================ # TARGET T0451 # 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 T0451.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 381 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.2564 0.1659 0.5777 2 M 0.2448 0.1572 0.5980 3 T 0.2319 0.1384 0.6297 4 H 0.1929 0.2108 0.5963 5 Y 0.1863 0.1754 0.6383 6 S 0.1512 0.1641 0.6847 7 D 0.0837 0.4206 0.4958 8 N 0.0635 0.4975 0.4390 9 T 0.0645 0.6080 0.3274 10 L 0.0342 0.7798 0.1860 11 K 0.0226 0.8566 0.1208 12 V 0.0189 0.8781 0.1030 13 A 0.0142 0.8907 0.0951 14 H 0.0092 0.9103 0.0805 15 Q 0.0089 0.9187 0.0725 16 G 0.0092 0.9185 0.0723 17 F 0.0083 0.9222 0.0695 18 E 0.0083 0.9237 0.0680 19 F 0.0084 0.9234 0.0682 20 F 0.0083 0.9218 0.0699 21 T 0.0084 0.9165 0.0751 22 Q 0.0085 0.9148 0.0767 23 G 0.0092 0.8950 0.0958 24 L 0.0131 0.8302 0.1567 25 A 0.0199 0.7077 0.2724 26 T 0.0563 0.3581 0.5856 27 G 0.0462 0.2000 0.7537 28 E 0.0959 0.3294 0.5747 29 W 0.0144 0.7749 0.2107 30 Q 0.0100 0.8709 0.1191 31 K 0.0089 0.9099 0.0811 32 F 0.0088 0.9085 0.0827 33 L 0.0090 0.9010 0.0901 34 D 0.0095 0.8636 0.1269 35 M 0.0129 0.7933 0.1938 36 L 0.0492 0.5029 0.4479 37 T 0.0730 0.3717 0.5554 38 E 0.0625 0.3563 0.5812 39 D 0.1309 0.2066 0.6625 40 F 0.3969 0.0813 0.5218 41 T 0.6367 0.0508 0.3125 42 F 0.7176 0.0272 0.2553 43 W 0.6334 0.0436 0.3230 44 F 0.5260 0.0303 0.4438 45 P 0.2893 0.1419 0.5688 46 M 0.2260 0.1299 0.6442 47 G 0.1838 0.0871 0.7291 48 E 0.1616 0.2162 0.6222 49 F 0.1786 0.2544 0.5670 50 H 0.1622 0.2217 0.6161 51 G 0.1606 0.1741 0.6653 52 L 0.1904 0.2969 0.5127 53 N 0.2047 0.3062 0.4891 54 V 0.1760 0.2723 0.5517 55 G 0.1093 0.3668 0.5239 56 K 0.0137 0.8019 0.1844 57 E 0.0093 0.8821 0.1087 58 R 0.0087 0.9179 0.0734 59 A 0.0085 0.9162 0.0753 60 K 0.0084 0.9188 0.0728 61 E 0.0084 0.9187 0.0729 62 F 0.0086 0.9098 0.0816 63 F 0.0091 0.9017 0.0892 64 T 0.0090 0.9026 0.0884 65 Y 0.0112 0.8670 0.1217 66 V 0.0205 0.7956 0.1839 67 S 0.0234 0.7639 0.2127 68 E 0.0262 0.7281 0.2457 69 S 0.0644 0.5317 0.4040 70 F 0.1128 0.3504 0.5368 71 H 0.0999 0.3123 0.5878 72 T 0.1175 0.2350 0.6475 73 G 0.1663 0.1305 0.7032 74 I 0.3382 0.1178 0.5440 75 Q 0.4706 0.0921 0.4373 76 I 0.5426 0.0707 0.3867 77 S 0.5480 0.0589 0.3932 78 S 0.5399 0.0545 0.4056 79 L 0.5129 0.1012 0.3859 80 D 0.5146 0.1198 0.3656 81 R 0.6715 0.0647 0.2639 82 V 0.6660 0.0484 0.2856 83 T 0.6225 0.0418 0.3357 84 S 0.4615 0.0890 0.4495 85 N 0.2383 0.0921 0.6696 86 E 0.1645 0.1009 0.7346 87 T 0.3682 0.0473 0.5844 88 T 0.7156 0.0141 0.2703 89 V 0.7743 0.0072 0.2184 90 V 0.8242 0.0064 0.1694 91 F 0.8222 0.0053 0.1725 92 E 0.8121 0.0087 0.1792 93 F 0.7796 0.0117 0.2087 94 R 0.7048 0.0307 0.2645 95 D 0.5620 0.0870 0.3510 96 E 0.4647 0.1121 0.4231 97 G 0.4994 0.1023 0.3983 98 L 0.5311 0.1131 0.3558 99 F 0.4570 0.1174 0.4256 100 L 0.2552 0.1029 0.6419 101 G 0.1745 0.0684 0.7570 102 K 0.3165 0.0317 0.6519 103 P 0.4144 0.0637 0.5219 104 Y 0.4280 0.0967 0.4753 105 K 0.3902 0.1155 0.4943 106 N 0.4733 0.0600 0.4667 107 R 0.6073 0.0398 0.3529 108 V 0.7807 0.0107 0.2086 109 A 0.8047 0.0056 0.1897 110 V 0.8222 0.0051 0.1728 111 S 0.8282 0.0040 0.1677 112 F 0.8203 0.0050 0.1747 113 D 0.7943 0.0051 0.2006 114 V 0.7473 0.0148 0.2380 115 R 0.5338 0.0476 0.4186 116 G 0.1633 0.0639 0.7728 117 D 0.1320 0.1001 0.7679 118 K 0.5458 0.0259 0.4283 119 I 0.6616 0.0308 0.3076 120 C 0.6361 0.0649 0.2989 121 S 0.7357 0.0374 0.2269 122 Y 0.6510 0.1051 0.2439 123 R 0.6236 0.1596 0.2168 124 E 0.5827 0.1851 0.2322 125 Y 0.4431 0.2122 0.3447 126 F 0.4062 0.1468 0.4470 127 G 0.2436 0.1003 0.6561 128 S 0.0947 0.3481 0.5572 129 D 0.0814 0.3534 0.5653 130 G 0.1023 0.3190 0.5787 131 K 0.1691 0.2343 0.5967 132 S 0.1971 0.1631 0.6398 133 N 0.1726 0.1289 0.6985