# This file is the result of combining several RDB files, specifically # T0482.t04.str2.rdb (weight 1.54425) # T0482.t04.str4.rdb (weight 0.924988) # T0482.t04.pb.rdb (weight 0.789901) # T0482.t04.bys.rdb (weight 0.748322) # T0482.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 T0482.t04.str2.rdb # ============================================ # TARGET T0482 # 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 T0482.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 5.74721 # # ============================================ # Comments from T0482.t04.str4.rdb # ============================================ # TARGET T0482 # 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 T0482.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 5.74721 # # ============================================ # Comments from T0482.t04.pb.rdb # ============================================ # TARGET T0482 # 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 T0482.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 5.74721 # # ============================================ # Comments from T0482.t04.bys.rdb # ============================================ # TARGET T0482 # 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 T0482.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 5.74721 # # ============================================ # Comments from T0482.t04.alpha.rdb # ============================================ # TARGET T0482 # 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 T0482.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 5.74721 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.2621 0.1608 0.5771 2 F 0.2855 0.0900 0.6245 3 E 0.2652 0.0580 0.6767 4 P 0.1910 0.1718 0.6372 5 G 0.2085 0.1576 0.6339 6 H 0.4144 0.0976 0.4880 7 L 0.5479 0.0978 0.3543 8 H 0.5995 0.0755 0.3250 9 L 0.5393 0.1325 0.3282 10 V 0.4449 0.1401 0.4150 11 S 0.3579 0.1021 0.5400 12 L 0.2579 0.0784 0.6637 13 P 0.1647 0.1688 0.6665 14 G 0.1374 0.1937 0.6688 15 L 0.2095 0.1465 0.6440 16 D 0.1957 0.0955 0.7088 17 Q 0.1504 0.2360 0.6136 18 Q 0.1444 0.2403 0.6154 19 D 0.2557 0.1309 0.6134 20 I 0.4311 0.0474 0.5215 21 N 0.5503 0.0279 0.4217 22 I 0.7156 0.0156 0.2688 23 H 0.7442 0.0118 0.2440 24 I 0.7787 0.0089 0.2124 25 R 0.7641 0.0132 0.2227 26 Y 0.7571 0.0125 0.2304 27 E 0.7134 0.0243 0.2623 28 V 0.6319 0.0657 0.3024 29 R 0.4939 0.1202 0.3859 30 Q 0.4463 0.1312 0.4225 31 N 0.3245 0.0721 0.6033 32 A 0.0885 0.3876 0.5239 33 E 0.0867 0.4035 0.5098 34 S 0.1158 0.1997 0.6844 35 G 0.1765 0.0830 0.7405 36 A 0.4235 0.0692 0.5072 37 Y 0.6947 0.0287 0.2766 38 V 0.7714 0.0141 0.2145 39 H 0.7900 0.0102 0.1999 40 F 0.7882 0.0094 0.2024 41 D 0.7286 0.0153 0.2560 42 M 0.6703 0.0446 0.2851 43 D 0.5518 0.0591 0.3890 44 G 0.5517 0.0486 0.3996 45 E 0.5944 0.0521 0.3535 46 I 0.5337 0.0605 0.4058 47 D 0.2289 0.0728 0.6984 48 G 0.1092 0.0675 0.8233 49 K 0.3405 0.0207 0.6388 50 P 0.4354 0.0259 0.5387 51 F 0.3775 0.0989 0.5236 52 S 0.2379 0.2086 0.5535 53 D 0.1796 0.3623 0.4581 54 S 0.2150 0.3142 0.4708 55 F 0.3799 0.1121 0.5080 56 E 0.3633 0.0716 0.5651 57 L 0.2710 0.0320 0.6970 58 P 0.1832 0.1156 0.7012 59 R 0.0659 0.4840 0.4502 60 D 0.0500 0.6429 0.3071 61 T 0.0510 0.7190 0.2299 62 A 0.0734 0.7305 0.1960 63 F 0.0585 0.7810 0.1605 64 N 0.0332 0.7898 0.1771 65 F 0.0202 0.8193 0.1605 66 A 0.0163 0.8436 0.1401 67 S 0.0126 0.8725 0.1150 68 D 0.0151 0.8700 0.1149 69 A 0.0109 0.8904 0.0987 70 T 0.0094 0.9120 0.0786 71 R 0.0089 0.9191 0.0720 72 V 0.0089 0.9192 0.0719 73 A 0.0104 0.9113 0.0784 74 Q 0.0113 0.8890 0.0997 75 K 0.0162 0.7526 0.2312 76 H 0.0606 0.2595 0.6799 77 G 0.0571 0.0969 0.8460 78 L 0.1640 0.0602 0.7758 79 H 0.1880 0.0387 0.7733 80 P 0.0889 0.4202 0.4909 81 K 0.0875 0.3750 0.5375 82 F 0.1364 0.3603 0.5032 83 G 0.1594 0.2859 0.5547 84 A 0.2007 0.3815 0.4178 85 I 0.1994 0.4602 0.3404 86 T 0.1659 0.5420 0.2921 87 R 0.1452 0.5685 0.2863 88 V 0.1030 0.5954 0.3017 89 H 0.0857 0.5924 0.3219 90 K 0.0310 0.7577 0.2113 91 E 0.0239 0.8098 0.1663 92 Y 0.0228 0.8515 0.1257 93 D 0.0183 0.8736 0.1080 94 A 0.0094 0.8850 0.1056 95 M 0.0118 0.8755 0.1127 96 F 0.0103 0.8883 0.1014 97 E 0.0090 0.9014 0.0896 98 D 0.0107 0.9041 0.0853 99 I 0.0098 0.8978 0.0924 100 R 0.0095 0.8994 0.0911 101 A 0.0108 0.8444 0.1449 102 K 0.0316 0.6674 0.3010 103 L 0.1322 0.3686 0.4992 104 H 0.1812 0.1511 0.6677 105 A 0.2353 0.0803 0.6844 106 H 0.1975 0.0351 0.7674 107 P 0.1019 0.2240 0.6742 108 G 0.0584 0.1942 0.7474 109 E 0.2478 0.0557 0.6964 110 P 0.3526 0.0300 0.6174 111 V 0.3838 0.0386 0.5776 112 D 0.2244 0.0157 0.7599 113 L 0.0366 0.6692 0.2942 114 E 0.0181 0.7941 0.1878 115 R 0.0513 0.7367 0.2120 116 I 0.1074 0.6824 0.2102 117 I 0.1556 0.5746 0.2698 118 R 0.1605 0.4242 0.4153 119 H 0.1277 0.2571 0.6152 120 E 0.1202 0.2023 0.6774