# This file is the result of combining several RDB files, specifically # T0301.t04.dssp-ebghstl.rdb (weight 1.53986) # T0301.t04.stride-ebghtl.rdb (weight 1.24869) # T0301.t04.str2.rdb (weight 1.54758) # T0301.t04.alpha.rdb (weight 0.659012) # 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 T0301.t04.dssp-ebghstl.rdb # ============================================ # TARGET T0301 # Using neural net t04-2621-IDGaaH13-3-13-7-13-9-13-11-ebghstl-dssp-seeded.net # This is a 4-layer network, with # window units # 3 13 # 7 13 # 9 13 # 11 7 (1 EBGHSTL ) # The input amino acid frequencies were determined from # alignment T0301.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 9.54204 # # ============================================ # Comments from T0301.t04.stride-ebghtl.rdb # ============================================ # TARGET T0301 # Using neural net t04-2621-IDGaaH13-3-13-7-13-9-13-11-ebghtl-stride-seeded.net # This is a 4-layer network, with # window units # 3 13 # 7 13 # 9 13 # 11 6 (1 EBGHTL ) # The input amino acid frequencies were determined from # alignment T0301.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 9.54204 # # ============================================ # Comments from T0301.t04.str2.rdb # ============================================ # TARGET T0301 # Using neural net dunbrack-30pc-1763-t2k-thin90-IDGaaH13-3-13-7-13-9-13-11-t1c2-str2-from-empty.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 T0301.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 9.54204 # # ============================================ # Comments from T0301.t04.alpha.rdb # ============================================ # TARGET T0301 # Using neural net t04-2621-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 T0301.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 9.54204 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.0814 0.0385 0.8801 2 A 0.1109 0.0416 0.8476 3 H 0.1001 0.0282 0.8716 4 P 0.0734 0.0418 0.8848 5 P 0.0856 0.1311 0.7834 6 Q 0.1983 0.1756 0.6262 7 I 0.3628 0.0887 0.5485 8 R 0.4481 0.0449 0.5070 9 I 0.3967 0.0229 0.5804 10 P 0.4063 0.0284 0.5653 11 A 0.6903 0.0518 0.2579 12 T 0.7649 0.0702 0.1649 13 Y 0.7665 0.0903 0.1431 14 L 0.6816 0.0821 0.2363 15 R 0.5040 0.0577 0.4383 16 G 0.2868 0.0606 0.6526 17 G 0.1455 0.0717 0.7828 18 T 0.1608 0.0850 0.7542 19 S 0.1702 0.0950 0.7348 20 K 0.1387 0.1657 0.6957 21 G 0.2368 0.1957 0.5675 22 V 0.4763 0.2347 0.2890 23 F 0.6018 0.1706 0.2276 24 F 0.6213 0.1271 0.2516 25 R 0.4821 0.1154 0.4026 26 L 0.0587 0.5997 0.3416 27 E 0.0206 0.5798 0.3996 28 D 0.0285 0.5319 0.4396 29 L 0.0806 0.1319 0.7875 30 P 0.0568 0.1879 0.7553 31 E 0.0294 0.5155 0.4550 32 S 0.0375 0.4277 0.5348 33 C 0.0839 0.2648 0.6512 34 R 0.0804 0.1228 0.7968 35 V 0.0603 0.0486 0.8910 36 P 0.0463 0.0956 0.8581 37 G 0.0272 0.2739 0.6988 38 E 0.0201 0.5386 0.4413 39 A 0.0199 0.7106 0.2695 40 R 0.0138 0.8232 0.1630 41 D 0.0117 0.8467 0.1415 42 R 0.0069 0.9239 0.0692 43 L 0.0085 0.9190 0.0725 44 F 0.0102 0.9272 0.0625 45 M 0.0119 0.9349 0.0532 46 R 0.0157 0.9203 0.0640 47 V 0.0226 0.8730 0.1045 48 I 0.0512 0.5583 0.3906 49 G 0.0799 0.1752 0.7448 50 S 0.1091 0.0549 0.8359 51 P 0.0740 0.0866 0.8395 52 D 0.0882 0.0588 0.8530 53 P 0.0152 0.3601 0.6247 54 Y 0.0210 0.3488 0.6302 55 A 0.0487 0.3937 0.5575 56 A 0.0867 0.2253 0.6881 57 H 0.2722 0.1605 0.5674 58 I 0.4163 0.1055 0.4782 59 D 0.2796 0.1075 0.6129 60 G 0.2289 0.0960 0.6751 61 M 0.2276 0.0955 0.6770 62 G 0.1875 0.0713 0.7412 63 G 0.1286 0.0650 0.8064 64 A 0.1618 0.0702 0.7680 65 T 0.1263 0.0634 0.8103 66 S 0.0934 0.1446 0.7620 67 S 0.0943 0.1486 0.7571 68 T 0.2019 0.0983 0.6999 69 S 0.2899 0.0415 0.6687 70 K 0.6328 0.0185 0.3487 71 C 0.8816 0.0050 0.1133 72 V 0.9192 0.0038 0.0770 73 I 0.9221 0.0033 0.0746 74 L 0.8698 0.0078 0.1224 75 S 0.5860 0.0119 0.4020 76 K 0.1667 0.1142 0.7190 77 S 0.0821 0.0879 0.8300 78 S 0.0883 0.0814 0.8303 79 Q 0.0658 0.0262 0.9080 80 P 0.0320 0.0971 0.8709 81 G 0.0393 0.1320 0.8287 82 H 0.1489 0.0943 0.7568 83 D 0.3298 0.0604 0.6098 84 V 0.5487 0.0739 0.3775 85 D 0.5847 0.0898 0.3255 86 Y 0.7912 0.0427 0.1661 87 L 0.8431 0.0290 0.1279 88 Y 0.8444 0.0286 0.1270 89 G 0.8128 0.0259 0.1613 90 Q 0.8276 0.0203 0.1521 91 V 0.8191 0.0284 0.1524 92 S 0.7975 0.0126 0.1899 93 I 0.5812 0.0398 0.3790 94 D 0.2322 0.0535 0.7143 95 K 0.1516 0.0657 0.7827 96 P 0.1798 0.1239 0.6963 97 F 0.4851 0.1086 0.4063 98 V 0.6577 0.0426 0.2997 99 D 0.4627 0.0351 0.5021 100 W 0.1883 0.1272 0.6845 101 S 0.1293 0.0897 0.7810 102 G 0.0784 0.1134 0.8082 103 N 0.0882 0.1166 0.7952 104 C 0.1574 0.1716 0.6710 105 G 0.1221 0.2115 0.6664 106 N 0.1469 0.3307 0.5224 107 L 0.1560 0.5462 0.2978 108 S 0.1777 0.5678 0.2544 109 T 0.1407 0.5985 0.2608 110 G 0.1220 0.5894 0.2886 111 A 0.1132 0.6183 0.2685 112 G 0.0531 0.6768 0.2701 113 A 0.0214 0.8555 0.1231 114 F 0.0464 0.8437 0.1098 115 A 0.0784 0.8099 0.1117 116 L 0.0968 0.7633 0.1400 117 H 0.0643 0.6816 0.2541 118 A 0.0627 0.3568 0.5804 119 G 0.0563 0.0721 0.8716 120 L 0.1436 0.0379 0.8184 121 V 0.3354 0.0229 0.6417 122 D 0.1382 0.0235 0.8383 123 P 0.0287 0.5569 0.4144 124 A 0.0372 0.5073 0.4554 125 R 0.1890 0.3491 0.4618 126 I 0.2349 0.0396 0.7255 127 P 0.1142 0.0624 0.8234 128 E 0.0477 0.1138 0.8384 129 D 0.0629 0.0659 0.8712 130 G 0.1252 0.0437 0.8311 131 I 0.6542 0.0164 0.3294 132 C 0.8643 0.0064 0.1292 133 E 0.9178 0.0047 0.0776 134 V 0.9238 0.0039 0.0723 135 R 0.9236 0.0051 0.0713 136 I 0.9150 0.0082 0.0767 137 W 0.8533 0.0237 0.1231 138 Q 0.7544 0.0334 0.2122 139 A 0.4420 0.1402 0.4178 140 N 0.2269 0.1299 0.6432 141 I 0.1197 0.1051 0.7752 142 G 0.1337 0.0864 0.7798 143 K 0.5474 0.0541 0.3985 144 T 0.8494 0.0227 0.1278 145 I 0.8993 0.0140 0.0867 146 I 0.9033 0.0122 0.0845 147 A 0.8847 0.0119 0.1034 148 H 0.8570 0.0106 0.1324 149 V 0.8353 0.0065 0.1582 150 P 0.8089 0.0047 0.1864 151 V 0.5132 0.0180 0.4688 152 S 0.2188 0.0533 0.7279 153 G 0.0621 0.0367 0.9013 154 G 0.1732 0.0327 0.7941 155 Q 0.6502 0.0161 0.3337 156 V 0.8599 0.0085 0.1315 157 Q 0.8179 0.0181 0.1640 158 E 0.7874 0.0261 0.1865 159 T 0.5591 0.0315 0.4093 160 G 0.3990 0.0286 0.5725 161 D 0.5435 0.0259 0.4306 162 F 0.7555 0.0202 0.2243 163 E 0.7638 0.0208 0.2154 164 L 0.7416 0.0254 0.2330 165 D 0.3974 0.0574 0.5452 166 G 0.1610 0.0362 0.8029 167 V 0.3800 0.0254 0.5946 168 T 0.3962 0.0266 0.5772 169 F 0.2067 0.0374 0.7559 170 P 0.1492 0.0876 0.7632 171 A 0.1323 0.2292 0.6386 172 A 0.2493 0.1416 0.6091 173 E 0.5035 0.0897 0.4068 174 I 0.7935 0.0287 0.1778 175 V 0.8387 0.0282 0.1331 176 L 0.8519 0.0243 0.1238 177 E 0.7727 0.0284 0.1990 178 F 0.6677 0.0290 0.3034 179 L 0.3890 0.0392 0.5717 180 D 0.1459 0.0235 0.8306 181 P 0.0426 0.1205 0.8369 182 S 0.0586 0.0858 0.8555 183 D 0.0471 0.0480 0.9049