# This file is the result of combining several RDB files, specifically # TR389.t04.str2.rdb (weight 1.54425) # TR389.t04.str4.rdb (weight 0.924988) # TR389.t04.pb.rdb (weight 0.789901) # TR389.t04.bys.rdb (weight 0.748322) # TR389.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 TR389.t04.str2.rdb # ============================================ # TARGET TR389 # 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 TR389.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 1713 # # ============================================ # Comments from TR389.t04.str4.rdb # ============================================ # TARGET TR389 # 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 TR389.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 1713 # # ============================================ # Comments from TR389.t04.pb.rdb # ============================================ # TARGET TR389 # 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 TR389.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 1713 # # ============================================ # Comments from TR389.t04.bys.rdb # ============================================ # TARGET TR389 # 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 TR389.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 1713 # # ============================================ # Comments from TR389.t04.alpha.rdb # ============================================ # TARGET TR389 # 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 TR389.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 1713 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.2993 0.0696 0.6312 2 I 0.2763 0.0724 0.6514 3 G 0.2610 0.0987 0.6402 4 T 0.3209 0.1360 0.5431 5 Q 0.4363 0.0670 0.4968 6 I 0.3576 0.0494 0.5930 7 V 0.1885 0.0230 0.7885 8 T 0.0158 0.7174 0.2668 9 E 0.0095 0.8653 0.1253 10 R 0.0088 0.9129 0.0783 11 L 0.0085 0.9190 0.0726 12 V 0.0084 0.9191 0.0726 13 A 0.0084 0.9174 0.0742 14 L 0.0088 0.9024 0.0888 15 L 0.0115 0.8499 0.1386 16 E 0.0164 0.6483 0.3353 17 S 0.0607 0.2444 0.6950 18 G 0.0615 0.0919 0.8466 19 T 0.1709 0.0835 0.7456 20 E 0.2120 0.1215 0.6665 21 K 0.4109 0.0581 0.5310 22 V 0.6983 0.0083 0.2934 23 L 0.7709 0.0071 0.2220 24 L 0.7933 0.0048 0.2018 25 I 0.7813 0.0109 0.2079 26 D 0.6698 0.0130 0.3172 27 S 0.4184 0.0514 0.5302 28 R 0.3019 0.0350 0.6631 29 P 0.1857 0.0579 0.7564 30 F 0.0711 0.5037 0.4251 31 V 0.0489 0.6797 0.2714 32 E 0.0539 0.7459 0.2002 33 Y 0.0776 0.6697 0.2527 34 N 0.0841 0.5910 0.3249 35 T 0.0946 0.4792 0.4262 36 S 0.1468 0.2952 0.5580 37 H 0.2518 0.1959 0.5523 38 I 0.2862 0.1479 0.5659 39 L 0.1976 0.2564 0.5459 40 E 0.2068 0.1806 0.6125 41 A 0.3582 0.1405 0.5013 42 I 0.5447 0.0911 0.3641 43 N 0.5376 0.0527 0.4097 44 I 0.4655 0.0585 0.4760 45 N 0.2952 0.0456 0.6592 46 C 0.0988 0.5075 0.3938 47 S 0.0316 0.7166 0.2518 48 K 0.0243 0.8031 0.1726 49 L 0.0258 0.8173 0.1568 50 M 0.0296 0.8091 0.1613 51 K 0.0350 0.7673 0.1978 52 R 0.0515 0.6850 0.2635 53 R 0.0748 0.5799 0.3452 54 L 0.1074 0.4657 0.4269 55 Q 0.1040 0.4076 0.4883 56 Q 0.1196 0.3434 0.5370 57 D 0.1038 0.3342 0.5621 58 K 0.1518 0.3329 0.5153 59 V 0.2318 0.2597 0.5085 60 L 0.2523 0.2046 0.5431 61 I 0.2259 0.2536 0.5205 62 T 0.1510 0.3280 0.5210 63 E 0.0287 0.7263 0.2449 64 L 0.0203 0.8196 0.1601 65 I 0.0222 0.8597 0.1181 66 Q 0.0183 0.8658 0.1159 67 H 0.0168 0.8726 0.1105 68 S 0.0163 0.8658 0.1178 69 A 0.0196 0.8283 0.1521 70 K 0.0297 0.7677 0.2026 71 H 0.0402 0.6841 0.2756 72 K 0.0832 0.4902 0.4266 73 V 0.1854 0.2174 0.5972 74 D 0.1964 0.1136 0.6900 75 I 0.2658 0.0997 0.6344 76 D 0.2144 0.0599 0.7257 77 C 0.1052 0.2487 0.6461 78 S 0.1231 0.1186 0.7584 79 Q 0.3659 0.0271 0.6070 80 K 0.6123 0.0127 0.3750 81 V 0.7945 0.0058 0.1997 82 V 0.8009 0.0057 0.1934 83 V 0.8042 0.0059 0.1899 84 Y 0.7599 0.0100 0.2301 85 D 0.4540 0.0158 0.5303 86 Q 0.1697 0.2326 0.5977 87 S 0.1300 0.1866 0.6835 88 S 0.1536 0.1828 0.6637 89 Q 0.0898 0.3535 0.5567 90 D 0.1084 0.3893 0.5023 91 V 0.1309 0.3579 0.5112 92 A 0.1330 0.2932 0.5737 93 S 0.1098 0.3284 0.5618 94 L 0.1073 0.3834 0.5092 95 S 0.0925 0.4705 0.4369 96 S 0.0443 0.6866 0.2691 97 D 0.0165 0.8262 0.1572 98 C 0.0098 0.8978 0.0925 99 F 0.0090 0.9138 0.0772 100 L 0.0086 0.9193 0.0720 101 T 0.0083 0.9217 0.0700 102 V 0.0084 0.9209 0.0708 103 L 0.0087 0.9116 0.0797 104 L 0.0094 0.9015 0.0891 105 G 0.0102 0.8780 0.1118 106 K 0.0179 0.7762 0.2058 107 L 0.0676 0.3992 0.5332 108 E 0.0611 0.1561 0.7827 109 K 0.1590 0.1207 0.7204 110 S 0.1636 0.1483 0.6881 111 F 0.2024 0.1424 0.6552 112 N 0.2442 0.1376 0.6181 113 S 0.4015 0.0660 0.5325 114 V 0.6634 0.0195 0.3171 115 H 0.7389 0.0167 0.2444 116 L 0.7446 0.0180 0.2374 117 L 0.5560 0.0836 0.3604 118 A 0.2863 0.1865 0.5272 119 G 0.1598 0.2218 0.6184 120 G 0.1261 0.3656 0.5083 121 F 0.0553 0.6906 0.2541 122 A 0.0239 0.8358 0.1402 123 E 0.0191 0.8707 0.1102 124 F 0.0176 0.8560 0.1264 125 S 0.0211 0.8279 0.1510 126 R 0.0305 0.7321 0.2374 127 C 0.0741 0.4205 0.5054 128 F 0.1562 0.1475 0.6963 129 P 0.1128 0.2525 0.6347 130 G 0.1264 0.2410 0.6326 131 L 0.2155 0.1965 0.5881 132 C 0.2806 0.1405 0.5789 133 E 0.2299 0.1273 0.6428 134 G 0.1485 0.0964 0.7551 135 K 0.1788 0.1189 0.7023