# This file is the result of combining several RDB files, specifically # T0523.t04.str2.rdb (weight 1.54425) # T0523.t04.str4.rdb (weight 0.924988) # T0523.t04.pb.rdb (weight 0.789901) # T0523.t04.bys.rdb (weight 0.748322) # T0523.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 T0523.t04.str2.rdb # ============================================ # TARGET T0523 # 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 T0523.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 5880 # # ============================================ # Comments from T0523.t04.str4.rdb # ============================================ # TARGET T0523 # 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 T0523.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 5880 # # ============================================ # Comments from T0523.t04.pb.rdb # ============================================ # TARGET T0523 # 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 T0523.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 5880 # # ============================================ # Comments from T0523.t04.bys.rdb # ============================================ # TARGET T0523 # 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 T0523.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 5880 # # ============================================ # Comments from T0523.t04.alpha.rdb # ============================================ # TARGET T0523 # 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 T0523.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 5880 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 P 0.1101 0.2246 0.6654 2 A 0.0547 0.6352 0.3102 3 I 0.0475 0.7434 0.2091 4 D 0.0499 0.7846 0.1655 5 Y 0.0189 0.8648 0.1163 6 K 0.0123 0.8998 0.0879 7 T 0.0110 0.9100 0.0790 8 A 0.0127 0.8974 0.0899 9 F 0.0177 0.8690 0.1133 10 H 0.0237 0.8091 0.1673 11 L 0.0722 0.5064 0.4214 12 A 0.1974 0.1644 0.6382 13 P 0.1592 0.2258 0.6151 14 I 0.2748 0.1493 0.5758 15 G 0.6330 0.0369 0.3301 16 L 0.7709 0.0125 0.2167 17 V 0.8057 0.0062 0.1881 18 L 0.7857 0.0086 0.2057 19 S 0.6429 0.0275 0.3295 20 R 0.3452 0.0902 0.5646 21 D 0.1754 0.1349 0.6896 22 R 0.2123 0.0956 0.6922 23 V 0.4959 0.0548 0.4493 24 I 0.5822 0.0855 0.3322 25 E 0.5416 0.1314 0.3270 26 D 0.5030 0.1390 0.3580 27 C 0.3544 0.1313 0.5142 28 N 0.1905 0.1536 0.6559 29 D 0.0111 0.7470 0.2418 30 E 0.0093 0.8672 0.1235 31 L 0.0089 0.9053 0.0858 32 A 0.0090 0.9147 0.0763 33 A 0.0094 0.8951 0.0955 34 I 0.0153 0.7976 0.1871 35 F 0.0565 0.3687 0.5748 36 R 0.0463 0.1566 0.7972 37 C 0.1519 0.0999 0.7482 38 A 0.1747 0.0471 0.7782 39 R 0.0214 0.6651 0.3134 40 A 0.0143 0.7784 0.2073 41 D 0.0250 0.7694 0.2055 42 L 0.0703 0.6025 0.3272 43 I 0.1052 0.3256 0.5692 44 G 0.0866 0.1605 0.7529 45 R 0.2000 0.0756 0.7244 46 S 0.2182 0.0538 0.7280 47 F 0.0874 0.4603 0.4523 48 E 0.0946 0.5596 0.3458 49 V 0.1647 0.4898 0.3454 50 L 0.2858 0.2022 0.5120 51 Y 0.2823 0.0669 0.6508 52 P 0.1790 0.0652 0.7559 53 S 0.1368 0.1155 0.7477 54 S 0.0379 0.5606 0.4015 55 D 0.0281 0.6226 0.3493 56 E 0.0386 0.7161 0.2453 57 F 0.0231 0.8275 0.1494 58 E 0.0124 0.8852 0.1023 59 R 0.0128 0.8802 0.1070 60 I 0.0143 0.8705 0.1151 61 G 0.0113 0.8772 0.1115 62 E 0.0096 0.8904 0.1000 63 R 0.0124 0.8600 0.1276 64 I 0.0151 0.8296 0.1554 65 S 0.0147 0.8543 0.1310 66 P 0.0132 0.8913 0.0955 67 V 0.0130 0.8923 0.0947 68 M 0.0265 0.8418 0.1317 69 I 0.0488 0.7140 0.2371 70 A 0.0805 0.4034 0.5161 71 H 0.0927 0.1627 0.7446 72 G 0.1357 0.0955 0.7687 73 S 0.2335 0.1162 0.6503 74 Y 0.3159 0.1028 0.5812 75 A 0.3675 0.1475 0.4850 76 D 0.3578 0.2063 0.4359 77 D 0.4754 0.2021 0.3225 78 R 0.6524 0.0945 0.2531 79 I 0.7175 0.0553 0.2271 80 M 0.7350 0.0398 0.2252 81 K 0.6847 0.0479 0.2674 82 R 0.5122 0.0327 0.4552 83 A 0.1829 0.2240 0.5931 84 G 0.0802 0.1457 0.7741 85 G 0.1444 0.0676 0.7881 86 E 0.5286 0.0168 0.4545 87 L 0.6903 0.0098 0.2999 88 F 0.7498 0.0123 0.2379 89 W 0.7844 0.0069 0.2088 90 C 0.8030 0.0082 0.1889 91 H 0.8018 0.0080 0.1902 92 V 0.7819 0.0141 0.2040 93 T 0.7163 0.0286 0.2551 94 G 0.6304 0.0401 0.3294 95 R 0.6134 0.0284 0.3583 96 A 0.5262 0.0523 0.4215 97 L 0.3764 0.0863 0.5373 98 D 0.2117 0.0641 0.7242 99 R 0.0426 0.3927 0.5647 100 T 0.0623 0.2363 0.7014 101 A 0.1619 0.1043 0.7338 102 P 0.2344 0.1267 0.6389 103 L 0.3464 0.1948 0.4588 104 A 0.4235 0.1527 0.4238 105 A 0.5947 0.1031 0.3021 106 G 0.6667 0.0606 0.2727 107 V 0.7634 0.0353 0.2012 108 W 0.7623 0.0281 0.2096 109 T 0.6972 0.0696 0.2332 110 F 0.5093 0.1628 0.3280 111 E 0.3133 0.2669 0.4198 112 D 0.2214 0.3017 0.4769 113 L 0.0889 0.5474 0.3638 114 S 0.0574 0.6291 0.3135 115 A 0.0321 0.7813 0.1866 116 T 0.0318 0.7775 0.1907 117 R 0.0374 0.7875 0.1751 118 R 0.0744 0.6266 0.2990 119 V 0.1293 0.4022 0.4685 120 A 0.1532 0.2483 0.5985