# This file is the result of combining several RDB files, specifically # TR435.t04.str2.rdb (weight 1.54425) # TR435.t04.str4.rdb (weight 0.924988) # TR435.t04.pb.rdb (weight 0.789901) # TR435.t04.bys.rdb (weight 0.748322) # TR435.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 TR435.t04.str2.rdb # ============================================ # TARGET TR435 # 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 TR435.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 1060 # # ============================================ # Comments from TR435.t04.str4.rdb # ============================================ # TARGET TR435 # 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 TR435.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 1060 # # ============================================ # Comments from TR435.t04.pb.rdb # ============================================ # TARGET TR435 # 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 TR435.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 1060 # # ============================================ # Comments from TR435.t04.bys.rdb # ============================================ # TARGET TR435 # 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 TR435.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 1060 # # ============================================ # Comments from TR435.t04.alpha.rdb # ============================================ # TARGET TR435 # 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 TR435.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 1060 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 S 0.1861 0.1954 0.6185 2 R 0.2410 0.2865 0.4725 3 A 0.2830 0.3174 0.3996 4 R 0.3074 0.2911 0.4015 5 L 0.3383 0.1593 0.5024 6 S 0.2865 0.0863 0.6273 7 L 0.2755 0.0332 0.6912 8 P 0.2444 0.0379 0.7177 9 K 0.3020 0.1466 0.5514 10 Q 0.4423 0.0870 0.4708 11 L 0.6660 0.0191 0.3149 12 V 0.7306 0.0123 0.2571 13 L 0.7279 0.0107 0.2614 14 R 0.6196 0.0290 0.3513 15 Q 0.5074 0.0588 0.4338 16 S 0.3970 0.0896 0.5134 17 I 0.3238 0.1652 0.5110 18 V 0.2178 0.1876 0.5946 19 G 0.1616 0.1173 0.7210 20 A 0.2038 0.1591 0.6371 21 E 0.2608 0.1138 0.6253 22 V 0.4839 0.0707 0.4454 23 G 0.6066 0.0454 0.3480 24 V 0.7275 0.0401 0.2324 25 W 0.7092 0.0386 0.2522 26 T 0.6190 0.0502 0.3308 27 G 0.4458 0.0994 0.4548 28 E 0.4848 0.0842 0.4310 29 T 0.4760 0.0624 0.4616 30 I 0.3702 0.0269 0.6030 31 P 0.2090 0.0378 0.7532 32 V 0.1311 0.2628 0.6061 33 R 0.0879 0.1588 0.7533 34 T 0.3665 0.0541 0.5794 35 C 0.6080 0.0399 0.3521 36 F 0.6604 0.0367 0.3029 37 G 0.6234 0.0232 0.3534 38 P 0.5806 0.0879 0.3315 39 L 0.5383 0.0896 0.3721 40 I 0.4330 0.0908 0.4763 41 G 0.3521 0.0754 0.5725 42 Q 0.5369 0.0741 0.3890 43 Q 0.5934 0.0489 0.3577 44 S 0.4644 0.0655 0.4700 45 H 0.2867 0.0723 0.6410 46 S 0.1279 0.4395 0.4327 47 M 0.0644 0.6657 0.2700 48 E 0.0905 0.6940 0.2155 49 V 0.0855 0.7211 0.1934 50 A 0.0612 0.7449 0.1940 51 E 0.0692 0.6805 0.2503 52 W 0.1075 0.5354 0.3571 53 T 0.1237 0.4383 0.4379 54 D 0.1118 0.4368 0.4514 55 K 0.1112 0.4229 0.4659 56 A 0.1355 0.3613 0.5032 57 V 0.1044 0.4139 0.4817 58 N 0.1143 0.3247 0.5609 59 H 0.2187 0.2985 0.4827 60 I 0.3396 0.2437 0.4167 61 W 0.4422 0.2134 0.3445 62 K 0.5621 0.1709 0.2670 63 I 0.6199 0.1286 0.2515 64 Y 0.5734 0.1141 0.3125 65 H 0.4114 0.1442 0.4443 66 N 0.2226 0.1314 0.6461 67 G 0.1514 0.1074 0.7412 68 V 0.2515 0.0799 0.6686 69 L 0.3192 0.1040 0.5768 70 E 0.3995 0.1009 0.4996 71 F 0.6494 0.0369 0.3138 72 C 0.7254 0.0179 0.2567 73 I 0.7434 0.0160 0.2406 74 I 0.6115 0.0297 0.3587 75 T 0.3859 0.1001 0.5140 76 T 0.2468 0.1139 0.6393 77 D 0.1517 0.2607 0.5877 78 E 0.0870 0.3742 0.5388 79 N 0.1140 0.2952 0.5908 80 E 0.1319 0.2983 0.5698 81 C 0.1464 0.3527 0.5009 82 N 0.1455 0.4373 0.4172 83 W 0.0953 0.6490 0.2557 84 M 0.1012 0.7296 0.1691 85 M 0.1242 0.7316 0.1441 86 F 0.1474 0.6796 0.1730 87 V 0.1765 0.6179 0.2056 88 R 0.1387 0.5282 0.3331 89 K 0.1104 0.4211 0.4686 90 A 0.1294 0.3063 0.5643 91 R 0.1535 0.2132 0.6333 92 N 0.1793 0.0789 0.7418 93 R 0.0434 0.4426 0.5139 94 E 0.0698 0.3455 0.5847 95 E 0.1859 0.3735 0.4406 96 Q 0.3284 0.2430 0.4286 97 N 0.4855 0.1259 0.3886 98 L 0.6224 0.0625 0.3151 99 V 0.7237 0.0320 0.2443 100 A 0.7058 0.0241 0.2701 101 Y 0.6031 0.0182 0.3788 102 P 0.4207 0.1051 0.4742 103 H 0.1845 0.1611 0.6544 104 D 0.1273 0.1020 0.7707 105 G 0.1846 0.0598 0.7556 106 K 0.5550 0.0172 0.4278 107 I 0.7621 0.0065 0.2314 108 F 0.8146 0.0061 0.1793 109 F 0.8240 0.0042 0.1718 110 C 0.8095 0.0076 0.1829 111 T 0.7535 0.0117 0.2349 112 S 0.5965 0.0594 0.3441 113 Q 0.4839 0.0874 0.4286 114 D 0.4138 0.0577 0.5285 115 I 0.3396 0.0276 0.6329 116 P 0.1884 0.0184 0.7932 117 P 0.0926 0.2585 0.6488 118 E 0.0438 0.1645 0.7917 119 N 0.2849 0.1460 0.5691 120 E 0.5987 0.0502 0.3511 121 L 0.7536 0.0245 0.2219 122 L 0.7744 0.0219 0.2037 123 F 0.7634 0.0214 0.2152 124 Y 0.5770 0.0695 0.3536 125 Y 0.3944 0.1454 0.4602 126 S 0.2431 0.1662 0.5906 127 R 0.1156 0.4004 0.4840 128 D 0.1067 0.4962 0.3972 129 Y 0.0624 0.6787 0.2589 130 A 0.0411 0.7406 0.2183 131 Q 0.0411 0.7409 0.2180 132 Q 0.0712 0.6089 0.3199 133 I 0.1039 0.2931 0.6030 134 G 0.0799 0.1109 0.8092 135 V 0.1885 0.0294 0.7821 136 P 0.1780 0.0594 0.7626 137 E 0.1754 0.1479 0.6767