# This file is the result of combining several RDB files, specifically # T0500.t04.str2.rdb (weight 1.54425) # T0500.t04.str4.rdb (weight 0.924988) # T0500.t04.pb.rdb (weight 0.789901) # T0500.t04.bys.rdb (weight 0.748322) # T0500.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 T0500.t04.str2.rdb # ============================================ # TARGET T0500 # 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 T0500.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 4.21594 # # ============================================ # Comments from T0500.t04.str4.rdb # ============================================ # TARGET T0500 # 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 T0500.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 4.21594 # # ============================================ # Comments from T0500.t04.pb.rdb # ============================================ # TARGET T0500 # 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 T0500.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 4.21594 # # ============================================ # Comments from T0500.t04.bys.rdb # ============================================ # TARGET T0500 # 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 T0500.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 4.21594 # # ============================================ # Comments from T0500.t04.alpha.rdb # ============================================ # TARGET T0500 # 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 T0500.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 4.21594 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 T 0.2108 0.1302 0.6590 2 D 0.1990 0.1353 0.6657 3 L 0.1164 0.4469 0.4367 4 A 0.1280 0.3893 0.4827 5 H 0.1723 0.2008 0.6269 6 L 0.2511 0.0540 0.6949 7 P 0.2065 0.0489 0.7446 8 P 0.2353 0.1138 0.6509 9 L 0.2675 0.0362 0.6963 10 P 0.2258 0.0274 0.7468 11 P 0.1960 0.0390 0.7651 12 P 0.1478 0.1486 0.7036 13 E 0.1291 0.1961 0.6748 14 G 0.1574 0.1503 0.6923 15 E 0.2507 0.1014 0.6479 16 A 0.3013 0.1650 0.5337 17 R 0.2897 0.1093 0.6010 18 K 0.3380 0.0375 0.6245 19 P 0.2730 0.0639 0.6631 20 A 0.2765 0.0755 0.6481 21 K 0.2879 0.0413 0.6708 22 P 0.2682 0.0390 0.6929 23 P 0.2494 0.0726 0.6780 24 V 0.2832 0.0780 0.6389 25 S 0.2347 0.0389 0.7264 26 P 0.2192 0.1402 0.6407 27 K 0.2927 0.1346 0.5727 28 P 0.2996 0.1525 0.5479 29 V 0.3395 0.2251 0.4355 30 L 0.3740 0.2524 0.3736 31 T 0.3986 0.1704 0.4311 32 Q 0.4004 0.0577 0.5419 33 P 0.3236 0.0696 0.6067 34 V 0.2894 0.0641 0.6465 35 P 0.2042 0.1731 0.6228 36 K 0.1942 0.3361 0.4697 37 L 0.2104 0.2636 0.5260 38 Q 0.1892 0.1721 0.6387 39 G 0.1859 0.0798 0.7343 40 S 0.2186 0.0446 0.7368 41 P 0.2536 0.0980 0.6484 42 T 0.2891 0.0493 0.6616 43 P 0.2399 0.1147 0.6454 44 T 0.2270 0.1731 0.5999 45 S 0.2404 0.1520 0.6076 46 K 0.2372 0.1722 0.5906 47 K 0.3340 0.0947 0.5713 48 V 0.4442 0.0237 0.5321 49 P 0.3884 0.0348 0.5768 50 L 0.4323 0.0333 0.5344 51 P 0.2720 0.0897 0.6384 52 G 0.2616 0.0621 0.6762 53 P 0.1655 0.1238 0.7107 54 G 0.1639 0.1024 0.7338 55 S 0.2186 0.0485 0.7329 56 P 0.2260 0.1352 0.6388 57 E 0.3037 0.1280 0.5683 58 V 0.3515 0.1826 0.4659 59 K 0.3761 0.2321 0.3919 60 R 0.3794 0.2521 0.3685 61 A 0.2537 0.3151 0.4312 62 H 0.1908 0.1478 0.6614 63 G 0.1268 0.0841 0.7891 64 T 0.2493 0.0263 0.7243 65 P 0.2547 0.0307 0.7146 66 P 0.3088 0.0395 0.6518 67 P 0.3215 0.0684 0.6101 68 V 0.3103 0.0599 0.6298 69 S 0.2531 0.0310 0.7159 70 P 0.2231 0.1086 0.6684 71 K 0.2867 0.0489 0.6644 72 P 0.2534 0.0329 0.7137 73 P 0.2398 0.0336 0.7266 74 P 0.2783 0.0406 0.6810 75 P 0.2372 0.0566 0.7062 76 P 0.2273 0.1427 0.6300 77 T 0.2460 0.0877 0.6663 78 A 0.2725 0.0514 0.6761 79 P 0.2575 0.0471 0.6954 80 K 0.3083 0.0390 0.6527 81 P 0.2961 0.0612 0.6426 82 V 0.2980 0.1986 0.5034 83 K 0.2972 0.3517 0.3512 84 A 0.3072 0.3659 0.3269 85 V 0.3083 0.2940 0.3977 86 A 0.2672 0.2162 0.5166 87 G 0.2313 0.1267 0.6421 88 L 0.2497 0.0514 0.6989 89 P 0.2226 0.1190 0.6584 90 S 0.2147 0.1249 0.6604 91 G 0.2032 0.1191 0.6777 92 S 0.2179 0.0869 0.6951 93 A 0.2276 0.1311 0.6414 94 G 0.2297 0.0618 0.7086 95 P 0.2185 0.1150 0.6665 96 S 0.2499 0.0514 0.6987 97 P 0.2357 0.0836 0.6807 98 A 0.2604 0.0566 0.6830 99 P 0.2543 0.0794 0.6663 100 S 0.2331 0.0497 0.7171 101 P 0.1467 0.2359 0.6175 102 A 0.1274 0.3763 0.4962 103 R 0.1531 0.2243 0.6227 104 Q 0.2518 0.0764 0.6718 105 P 0.1996 0.0510 0.7494 106 P 0.1712 0.2625 0.5663 107 A 0.1636 0.4122 0.4242 108 A 0.2131 0.3646 0.4223 109 L 0.3191 0.2082 0.4727 110 A 0.3291 0.0979 0.5731 111 K 0.3002 0.0410 0.6588 112 P 0.1849 0.0357 0.7793 113 P 0.1332 0.1755 0.6913 114 G 0.1020 0.1271 0.7709 115 T 0.2028 0.0470 0.7502 116 P 0.2059 0.0493 0.7449 117 P 0.2176 0.1654 0.6171 118 S 0.1988 0.1531 0.6481 119 L 0.2197 0.1186 0.6617 120 G 0.1955 0.1168 0.6877 121 A 0.2543 0.1165 0.6292 122 S 0.2411 0.0389 0.7200 123 P 0.2228 0.1721 0.6051 124 A 0.2459 0.1117 0.6425 125 K 0.2806 0.0418 0.6776 126 P 0.2358 0.0370 0.7272 127 P 0.2427 0.1105 0.6468 128 S 0.2167 0.0450 0.7383 129 P 0.1233 0.1786 0.6981 130 G 0.1079 0.1208 0.7713 131 A 0.2276 0.0376 0.7348 132 P 0.2141 0.0722 0.7137 133 A 0.2418 0.1700 0.5882 134 L 0.2298 0.1721 0.5981 135 H 0.2624 0.0915 0.6461 136 V 0.3071 0.0438 0.6491 137 P 0.2513 0.0611 0.6876 138 A 0.2626 0.0723 0.6651 139 K 0.2665 0.0481 0.6854 140 P 0.2207 0.0347 0.7445 141 P 0.1702 0.1598 0.6700 142 R 0.1066 0.4812 0.4122 143 A 0.1069 0.5537 0.3395 144 A 0.1353 0.5691 0.2956 145 A 0.1998 0.4883 0.3119 146 A 0.2500 0.4302 0.3198 147 A 0.2968 0.3679 0.3353 148 A 0.3215 0.3359 0.3426 149 A 0.3415 0.2838 0.3747 150 A 0.2714 0.3271 0.4015 151 A 0.2236 0.2697 0.5067 152 A 0.2221 0.1767 0.6012 153 A 0.2238 0.0665 0.7097 154 P 0.2105 0.0486 0.7408 155 P 0.2387 0.0754 0.6859 156 A 0.2545 0.0423 0.7031 157 P 0.2057 0.0307 0.7636 158 P 0.1681 0.1691 0.6629 159 E 0.1311 0.2267 0.6422 160 G 0.1458 0.1551 0.6991 161 A 0.2217 0.0893 0.6890 162 S 0.2175 0.0438 0.7387 163 P 0.1503 0.2012 0.6486 164 G 0.0894 0.3387 0.5719 165 D 0.0649 0.5566 0.3785 166 S 0.0504 0.7147 0.2349 167 A 0.0334 0.8053 0.1613 168 R 0.0350 0.8357 0.1293 169 Q 0.0424 0.8172 0.1403 170 K 0.0624 0.7513 0.1862 171 L 0.0678 0.7344 0.1978 172 E 0.0463 0.7728 0.1809 173 E 0.0646 0.7198 0.2156 174 T 0.0692 0.6007 0.3301 175 S 0.0298 0.7416 0.2287 176 A 0.0140 0.8642 0.1217 177 C 0.0150 0.8745 0.1105 178 L 0.0086 0.9080 0.0834 179 A 0.0084 0.9166 0.0750 180 A 0.0085 0.9173 0.0742 181 A 0.0088 0.9079 0.0833 182 L 0.0089 0.9076 0.0836 183 Q 0.0100 0.9004 0.0897 184 A 0.0137 0.8811 0.1052 185 V 0.0142 0.8696 0.1162 186 E 0.0113 0.8827 0.1059 187 E 0.0142 0.8747 0.1111 188 K 0.0429 0.7875 0.1697 189 I 0.0878 0.6526 0.2596 190 R 0.0920 0.5458 0.3622 191 Q 0.1202 0.5464 0.3334 192 E 0.1172 0.4552 0.4276 193 D 0.1407 0.2968 0.5625 194 A 0.1308 0.2948 0.5744 195 Q 0.1627 0.1822 0.6550 196 G 0.1786 0.0692 0.7522 197 P 0.1761 0.1290 0.6949 198 R 0.1955 0.1559 0.6486 199 D 0.1729 0.1696 0.6575 200 S 0.1838 0.1366 0.6796