# 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 14.1322 # # ============================================ # 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 14.1322 # # ============================================ # 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 14.1322 # # ============================================ # 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 14.1322 # # ============================================ # 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 14.1322 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 A 0.2028 0.3232 0.4740 2 E 0.2016 0.4126 0.3858 3 L 0.2114 0.5058 0.2828 4 Q 0.1680 0.5852 0.2468 5 K 0.1637 0.6033 0.2330 6 A 0.1218 0.6594 0.2188 7 E 0.0939 0.6692 0.2369 8 Y 0.1147 0.5805 0.3048 9 A 0.1385 0.4783 0.3832 10 K 0.1403 0.4266 0.4331 11 Y 0.1610 0.3548 0.4842 12 E 0.1435 0.2387 0.6178 13 G 0.1350 0.1496 0.7154 14 G 0.1810 0.0990 0.7200 15 P 0.1861 0.3048 0.5091 16 L 0.1824 0.4275 0.3901 17 R 0.1958 0.4011 0.4030 18 R 0.2127 0.2988 0.4885 19 K 0.2196 0.1598 0.6206 20 A 0.2006 0.0650 0.7344 21 P 0.1189 0.2216 0.6595 22 Q 0.1177 0.2835 0.5988 23 S 0.1832 0.3196 0.4972 24 L 0.2640 0.2782 0.4577 25 E 0.4973 0.1917 0.3111 26 V 0.6496 0.0944 0.2560 27 M 0.6843 0.0760 0.2397 28 A 0.7118 0.0559 0.2323 29 I 0.6529 0.0714 0.2757 30 E 0.5208 0.0770 0.4022 31 S 0.3161 0.0413 0.6426 32 P 0.2050 0.0454 0.7495 33 P 0.2243 0.0557 0.7200 34 P 0.1933 0.0435 0.7632 35 P 0.1798 0.1495 0.6708 36 E 0.2153 0.0781 0.7066 37 P 0.2269 0.0802 0.6929 38 T 0.2093 0.0348 0.7559 39 P 0.1456 0.2190 0.6354 40 A 0.1694 0.2292 0.6014 41 D 0.1902 0.1741 0.6357 42 C 0.1531 0.2351 0.6118 43 Q 0.1817 0.1778 0.6405 44 S 0.2078 0.1067 0.6855 45 P 0.1624 0.2813 0.5563 46 K 0.2081 0.2351 0.5568 47 M 0.2938 0.1590 0.5473 48 T 0.3586 0.1227 0.5186 49 T 0.4375 0.1237 0.4389 50 F 0.3900 0.1401 0.4699 51 Q 0.2709 0.1528 0.5762 52 D 0.1741 0.3158 0.5100 53 S 0.0397 0.6471 0.3133 54 E 0.0341 0.6639 0.3020 55 L 0.0641 0.4850 0.4508 56 S 0.0575 0.5446 0.3978 57 D 0.0103 0.8162 0.1735 58 E 0.0096 0.8793 0.1111 59 L 0.0090 0.9159 0.0751 60 Q 0.0090 0.9122 0.0788 61 A 0.0101 0.8809 0.1090 62 A 0.0195 0.8087 0.1719 63 M 0.0508 0.5432 0.4060 64 T 0.0961 0.2629 0.6410 65 G 0.1240 0.1268 0.7492 66 P 0.1165 0.2345 0.6490 67 A 0.1454 0.2799 0.5747 68 E 0.1577 0.2686 0.5737 69 V 0.2081 0.1991 0.5928 70 G 0.2103 0.0974 0.6922 71 P 0.1670 0.1971 0.6359 72 T 0.1944 0.2173 0.5884 73 T 0.2132 0.1713 0.6154 74 E 0.2607 0.1109 0.6285 75 K 0.2684 0.0425 0.6891 76 P 0.1959 0.0685 0.7356 77 S 0.1587 0.2429 0.5985 78 S 0.1542 0.2431 0.6027 79 H 0.1937 0.1281 0.6783 80 L 0.2626 0.0330 0.7044 81 P 0.2082 0.0326 0.7592 82 P 0.2303 0.1158 0.6540 83 T 0.2401 0.0424 0.7175 84 P 0.2083 0.2126 0.5791 85 R 0.2845 0.1714 0.5441 86 A 0.3567 0.1106 0.5327 87 T 0.3243 0.0705 0.6052 88 T 0.3087 0.1528 0.5385 89 R 0.2879 0.1394 0.5727 90 Q 0.2747 0.1198 0.6055 91 D 0.2381 0.0955 0.6664 92 S 0.1643 0.2291 0.6066 93 S 0.1526 0.2165 0.6309 94 L 0.1402 0.2034 0.6564 95 G 0.1478 0.1437 0.7085 96 G 0.1765 0.1271 0.6964 97 R 0.2768 0.1657 0.5575 98 A 0.3620 0.1870 0.4510 99 R 0.3632 0.2011 0.4358 100 H 0.3828 0.1375 0.4796 101 M 0.3110 0.0941 0.5949 102 S 0.2430 0.1126 0.6444 103 S 0.2712 0.1113 0.6176 104 S 0.2428 0.1767 0.5805 105 Q 0.2544 0.2906 0.4550 106 E 0.2699 0.3282 0.4020 107 L 0.2654 0.2723 0.4623 108 L 0.2238 0.1811 0.5951 109 G 0.1656 0.1350 0.6994 110 D 0.1967 0.0929 0.7104 111 G 0.2293 0.0557 0.7150 112 P 0.2173 0.0500 0.7327 113 P 0.2220 0.1005 0.6776 114 G 0.2186 0.0545 0.7269 115 P 0.1889 0.1228 0.6883 116 S 0.2330 0.0896 0.6773 117 S 0.2422 0.0416 0.7162 118 P 0.2148 0.1176 0.6676 119 M 0.2362 0.1468 0.6170 120 S 0.2124 0.1116 0.6761 121 R 0.1411 0.2686 0.5903 122 S 0.1632 0.2371 0.5997 123 Q 0.2350 0.2406 0.5245 124 E 0.2894 0.2437 0.4669 125 Y 0.2980 0.2543 0.4476 126 L 0.2490 0.2330 0.5180 127 L 0.2460 0.1798 0.5741 128 D 0.2045 0.1335 0.6620 129 E 0.2010 0.1468 0.6522 130 G 0.2017 0.0579 0.7404 131 P 0.2126 0.0935 0.6939 132 A 0.2164 0.0642 0.7194 133 P 0.1495 0.1375 0.7131 134 G 0.1153 0.0938 0.7909 135 T 0.2307 0.0257 0.7437 136 P 0.2054 0.0230 0.7716 137 P 0.1904 0.0981 0.7115 138 R 0.1641 0.2982 0.5376 139 E 0.2204 0.2501 0.5295 140 A 0.2716 0.1214 0.6071 141 R 0.2684 0.0449 0.6867 142 P 0.2156 0.1327 0.6517 143 G 0.1711 0.1272 0.7018 144 R 0.1809 0.1617 0.6574 145 H 0.1909 0.1249 0.6842 146 G 0.1849 0.1377 0.6774 147 H 0.2567 0.0978 0.6455 148 S 0.2969 0.1092 0.5939 149 I 0.2663 0.1981 0.5355 150 K 0.2252 0.1836 0.5912 151 R 0.2035 0.2813 0.5152 152 A 0.2353 0.2137 0.5510 153 S 0.2475 0.1251 0.6274 154 V 0.3090 0.0411 0.6499 155 P 0.2198 0.0346 0.7456 156 P 0.2395 0.1056 0.6549 157 V 0.2370 0.0507 0.7123 158 P 0.1709 0.0813 0.7478 159 G 0.1553 0.0777 0.7671 160 K 0.2075 0.0321 0.7603 161 P 0.2293 0.0893 0.6814 162 R 0.2244 0.2205 0.5550 163 Q 0.3409 0.2006 0.4586 164 V 0.3966 0.0969 0.5065 165 L 0.3857 0.0305 0.5838 166 P 0.2402 0.0314 0.7284 167 P 0.1983 0.1640 0.6377 168 G 0.1772 0.1403 0.6825 169 T 0.2077 0.1257 0.6666 170 S 0.2076 0.1440 0.6484 171 H 0.1974 0.1722 0.6303 172 F 0.2441 0.1267 0.6292 173 T 0.2661 0.0488 0.6852 174 P 0.2207 0.0571 0.7222 175 P 0.2144 0.1470 0.6386 176 Q 0.2089 0.1213 0.6698 177 T 0.2621 0.0415 0.6964 178 P 0.2306 0.0913 0.6781 179 T 0.2761 0.1248 0.5991 180 K 0.2852 0.1290 0.5858 181 T 0.2830 0.0856 0.6314 182 R 0.2530 0.0400 0.7070 183 P 0.1919 0.1166 0.6916 184 G 0.1777 0.0916 0.7306 185 S 0.2167 0.0514 0.7319 186 P 0.1905 0.2063 0.6032 187 Q 0.2133 0.2662 0.5205 188 A 0.2449 0.2348 0.5202 189 L 0.2222 0.2054 0.5724 190 G 0.2130 0.1110 0.6760 191 G 0.2189 0.0548 0.7262 192 P 0.1865 0.1386 0.6749 193 H 0.2334 0.1059 0.6607 194 G 0.2119 0.0512 0.7370 195 P 0.2145 0.0786 0.7069 196 A 0.2331 0.0719 0.6950 197 P 0.1607 0.2247 0.6146 198 A 0.1512 0.2493 0.5995 199 T 0.1810 0.1591 0.6598 200 A 0.1975 0.1849 0.6176