# This file is the result of combining several RDB files, specifically # TR462.t2k.str2.rdb (weight 1.54425) # TR462.t2k.str4.rdb (weight 0.924988) # TR462.t2k.pb.rdb (weight 0.789901) # TR462.t2k.bys.rdb (weight 0.748322) # TR462.t2k.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 TR462.t2k.str2.rdb # ============================================ # TARGET TR462 # Using neural net dunbrack-40pc-3157-t2k-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 TR462.t2k-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 58.3675 # # ============================================ # Comments from TR462.t2k.str4.rdb # ============================================ # TARGET TR462 # Using neural net dunbrack-40pc-3157-t2k-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 TR462.t2k-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 58.3675 # # ============================================ # Comments from TR462.t2k.pb.rdb # ============================================ # TARGET TR462 # Using neural net dunbrack-40pc-3157-t2k-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 TR462.t2k-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 58.3675 # # ============================================ # Comments from TR462.t2k.bys.rdb # ============================================ # TARGET TR462 # Using neural net dunbrack-40pc-3157-t2k-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 TR462.t2k-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 58.3675 # # ============================================ # Comments from TR462.t2k.alpha.rdb # ============================================ # TARGET TR462 # Using neural net dunbrack-40pc-3157-t2k-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 TR462.t2k-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 58.3675 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.4967 0.0372 0.4661 2 K 0.3709 0.0342 0.5949 3 L 0.2407 0.4037 0.3557 4 S 0.1586 0.4870 0.3545 5 R 0.2844 0.2526 0.4630 6 L 0.3399 0.0824 0.5777 7 V 0.2537 0.0418 0.7045 8 P 0.1464 0.1245 0.7291 9 G 0.0526 0.1057 0.8417 10 V 0.2686 0.0206 0.7108 11 P 0.5452 0.0150 0.4398 12 A 0.6684 0.0147 0.3169 13 R 0.7839 0.0071 0.2090 14 I 0.7341 0.0073 0.2586 15 K 0.6639 0.0238 0.3123 16 R 0.7308 0.0176 0.2516 17 L 0.6267 0.0335 0.3398 18 E 0.5049 0.0539 0.4412 19 V 0.2813 0.0972 0.6215 20 S 0.1283 0.1945 0.6772 21 G 0.0482 0.4766 0.4751 22 E 0.0343 0.7435 0.2223 23 L 0.0269 0.8446 0.1285 24 H 0.0162 0.8937 0.0901 25 E 0.0128 0.9085 0.0787 26 K 0.0155 0.9022 0.0822 27 L 0.0188 0.8776 0.1036 28 V 0.0235 0.8159 0.1606 29 G 0.0564 0.6450 0.2987 30 M 0.0737 0.2762 0.6501 31 G 0.1279 0.0911 0.7810 32 F 0.2861 0.0456 0.6683 33 V 0.2891 0.0233 0.6875 34 P 0.2189 0.1091 0.6720 35 G 0.1056 0.0985 0.7959 36 E 0.4007 0.0362 0.5632 37 E 0.6897 0.0127 0.2976 38 I 0.7810 0.0078 0.2113 39 E 0.7989 0.0066 0.1945 40 I 0.7919 0.0071 0.2011 41 V 0.7547 0.0190 0.2262 42 Q 0.7395 0.0218 0.2387 43 V 0.6201 0.0531 0.3267 44 A 0.5483 0.0351 0.4166 45 P 0.3963 0.1369 0.4668 46 L 0.1565 0.1577 0.6858 47 G 0.1091 0.1231 0.7678 48 D 0.2260 0.0344 0.7397 49 P 0.3388 0.0571 0.6042 50 I 0.6336 0.0277 0.3387 51 V 0.7921 0.0078 0.2001 52 C 0.8017 0.0067 0.1916 53 K 0.7633 0.0069 0.2298 54 I 0.6544 0.0259 0.3197 55 G 0.3992 0.0465 0.5542 56 N 0.2518 0.0633 0.6849 57 R 0.4920 0.0466 0.4614 58 N 0.6823 0.0243 0.2934 59 I 0.7587 0.0183 0.2230 60 T 0.7441 0.0256 0.2303 61 L 0.6971 0.0535 0.2494 62 R 0.4934 0.1104 0.3962 63 K 0.2228 0.4334 0.3439 64 R 0.1003 0.5554 0.3443 65 E 0.1656 0.4286 0.4058 66 A 0.2705 0.3709 0.3586 67 D 0.3520 0.2454 0.4026 68 L 0.6034 0.0863 0.3103 69 I 0.7223 0.0194 0.2583 70 E 0.7493 0.0103 0.2404 71 V 0.7825 0.0078 0.2096 72 E 0.7428 0.0104 0.2468 73 V 0.6420 0.0213 0.3367 74 V 0.4109 0.0665 0.5226 75 G 0.2170 0.0991 0.6839 76 G 0.1654 0.1130 0.7216 77 E 0.2794 0.1085 0.6121 78 L 0.3406 0.0582 0.6012 79 P 0.3258 0.1058 0.5683 80 L 0.3954 0.1841 0.4205 81 I 0.4252 0.1879 0.3869 82 L 0.4035 0.1796 0.4169 83 A 0.2800 0.1994 0.5206 84 D 0.1737 0.2321 0.5942 85 D 0.1020 0.1742 0.7237 86 G 0.0922 0.1253 0.7826 87 T 0.2499 0.1059 0.6443 88 Y 0.3543 0.0836 0.5621 89 E 0.4445 0.1279 0.4275 90 I 0.4961 0.1492 0.3547 91 T 0.4798 0.1628 0.3574 92 K 0.4002 0.1885 0.4112 93 L 0.2696 0.2366 0.4938 94 N 0.1701 0.1821 0.6478 95 G 0.1165 0.1491 0.7344 96 G 0.1306 0.2177 0.6517 97 R 0.1882 0.3384 0.4734 98 R 0.1871 0.5105 0.3024 99 F 0.1349 0.6606 0.2044 100 L 0.0867 0.7591 0.1543 101 F 0.0679 0.7936 0.1385 102 R 0.0644 0.7769 0.1587 103 M 0.0671 0.7452 0.1877 104 K 0.0780 0.7033 0.2187 105 N 0.1137 0.5575 0.3287 106 L 0.1249 0.3133 0.5618 107 G 0.1211 0.1664 0.7125 108 I 0.1464 0.2649 0.5887 109 E 0.1890 0.2293 0.5817 110 S 0.1840 0.1329 0.6832 111 G 0.1796 0.0688 0.7516 112 K 0.3973 0.0233 0.5794 113 K 0.6921 0.0106 0.2973 114 I 0.7925 0.0070 0.2006 115 Q 0.7886 0.0078 0.2036 116 V 0.7550 0.0120 0.2330 117 S 0.5952 0.0324 0.3724 118 G 0.3442 0.0437 0.6122 119 R 0.2751 0.0712 0.6536 120 R 0.2396 0.2182 0.5421 121 Y 0.2419 0.2242 0.5339 122 Y 0.2659 0.1811 0.5531 123 I 0.2684 0.1306 0.6010 124 E 0.2197 0.1459 0.6344 125 G 0.2058 0.1258 0.6683 126 R 0.2892 0.1714 0.5394 127 E 0.4754 0.1738 0.3508 128 I 0.5652 0.1581 0.2767 129 D 0.4909 0.1659 0.3432 130 L 0.3243 0.3084 0.3673 131 G 0.2634 0.2728 0.4637 132 Y 0.2040 0.1981 0.5979 133 G 0.1529 0.1380 0.7091 134 E 0.1910 0.2172 0.5918 135 A 0.2445 0.1861 0.5695 136 T 0.3503 0.1065 0.5433 137 K 0.5833 0.0275 0.3892 138 I 0.7122 0.0092 0.2786 139 W 0.7775 0.0080 0.2145 140 V 0.7872 0.0106 0.2022 141 R 0.7493 0.0153 0.2355 142 R 0.6577 0.0163 0.3260 143 V 0.4557 0.0451 0.4992