# This file is the result of combining several RDB files, specifically # T0407.t2k.str2.rdb (weight 1.54425) # T0407.t2k.str4.rdb (weight 0.924988) # T0407.t2k.pb.rdb (weight 0.789901) # T0407.t2k.bys.rdb (weight 0.748322) # T0407.t2k.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 T0407.t2k.str2.rdb # ============================================ # TARGET T0407 # Using neural net dunbrack-40pc-3157-t2k-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 T0407.t2k-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 2 # # ============================================ # Comments from T0407.t2k.str4.rdb # ============================================ # TARGET T0407 # Using neural net dunbrack-40pc-3157-t2k-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 T0407.t2k-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 2 # # ============================================ # Comments from T0407.t2k.pb.rdb # ============================================ # TARGET T0407 # Using neural net dunbrack-40pc-3157-t2k-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 T0407.t2k-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 2 # # ============================================ # Comments from T0407.t2k.bys.rdb # ============================================ # TARGET T0407 # Using neural net dunbrack-40pc-3157-t2k-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 T0407.t2k-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 2 # # ============================================ # Comments from T0407.t2k.alpha.rdb # ============================================ # TARGET T0407 # Using neural net dunbrack-40pc-3157-t2k-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 T0407.t2k-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 2 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 A 0.2577 0.4108 0.3314 2 A 0.2814 0.4385 0.2801 3 Y 0.2911 0.4581 0.2508 4 F 0.2615 0.4894 0.2491 5 H 0.1925 0.5823 0.2252 6 E 0.2065 0.5755 0.2180 7 L 0.2487 0.4986 0.2527 8 L 0.2734 0.3894 0.3372 9 I 0.2439 0.2988 0.4573 10 G 0.1728 0.1883 0.6389 11 R 0.0747 0.4841 0.4413 12 E 0.0299 0.7115 0.2587 13 D 0.0279 0.7471 0.2250 14 L 0.0333 0.7231 0.2436 15 L 0.0666 0.6119 0.3216 16 R 0.0800 0.5294 0.3906 17 P 0.0284 0.7344 0.2372 18 F 0.0336 0.6854 0.2810 19 F 0.0469 0.7460 0.2070 20 E 0.0474 0.7293 0.2233 21 K 0.0971 0.5722 0.3307 22 C 0.1988 0.3854 0.4158 23 V 0.3330 0.2440 0.4230 24 K 0.3473 0.1772 0.4755 25 I 0.2497 0.3975 0.3529 26 E 0.2477 0.4060 0.3463 27 E 0.3674 0.2853 0.3473 28 V 0.4206 0.2045 0.3749 29 S 0.3773 0.1598 0.4629 30 R 0.2730 0.2521 0.4749 31 N 0.1810 0.2225 0.5965 32 E 0.1760 0.2826 0.5414 33 Q 0.1583 0.1745 0.6671 34 G 0.2381 0.0810 0.6810 35 V 0.4834 0.0212 0.4954 36 T 0.6754 0.0154 0.3092 37 L 0.7365 0.0167 0.2468 38 S 0.7329 0.0177 0.2494 39 I 0.6539 0.0494 0.2967 40 T 0.5101 0.0922 0.3976 41 N 0.3618 0.0939 0.5443 42 V 0.2052 0.3537 0.4411 43 T 0.1803 0.4308 0.3890 44 D 0.2031 0.4911 0.3058 45 L 0.2730 0.5097 0.2173 46 V 0.3323 0.4732 0.1946 47 L 0.4342 0.3799 0.1859 48 K 0.4415 0.3269 0.2316 49 L 0.3525 0.3479 0.2996 50 K 0.2656 0.3610 0.3734 51 K 0.2166 0.3399 0.4435 52 T 0.1839 0.2726 0.5435 53 A 0.1467 0.3019 0.5514 54 H 0.1454 0.2570 0.5976 55 D 0.1725 0.2112 0.6163 56 T 0.1569 0.3634 0.4798 57 L 0.3197 0.2902 0.3901 58 L 0.5301 0.1916 0.2782 59 V 0.6731 0.1110 0.2160 60 Y 0.6724 0.1027 0.2249 61 F 0.6054 0.1309 0.2637 62 R 0.4461 0.2388 0.3151 63 D 0.3639 0.2101 0.4260 64 M 0.3714 0.1391 0.4895 65 T 0.3746 0.0886 0.5369 66 L 0.3908 0.0728 0.5363 67 K 0.3299 0.0390 0.6311 68 P 0.2636 0.1363 0.6001 69 H 0.2579 0.1172 0.6249 70 T 0.3335 0.0907 0.5758 71 R 0.4170 0.0911 0.4919 72 Y 0.6241 0.0419 0.3340 73 T 0.7335 0.0154 0.2511 74 V 0.7751 0.0131 0.2118 75 R 0.7692 0.0123 0.2186 76 I 0.7492 0.0222 0.2286 77 G 0.6686 0.0389 0.2925 78 F 0.5511 0.0840 0.3649 79 K 0.3158 0.1831 0.5011 80 Q 0.1574 0.1526 0.6900 81 G 0.1505 0.0810 0.7686 82 I 0.3293 0.0586 0.6121 83 K 0.2986 0.0829 0.6185 84 G 0.2136 0.1044 0.6819 85 G 0.1970 0.1218 0.6811 86 D 0.2793 0.0937 0.6269 87 V 0.3571 0.1214 0.5215 88 N 0.3848 0.0908 0.5244 89 F 0.4847 0.0713 0.4440 90 E 0.6105 0.0418 0.3478 91 V 0.6085 0.0435 0.3480 92 T 0.5164 0.0688 0.4148 93 N 0.5720 0.0517 0.3763 94 F 0.6819 0.0323 0.2858 95 I 0.7324 0.0194 0.2482 96 V 0.6901 0.0229 0.2870 97 A 0.4600 0.0202 0.5198 98 P 0.2304 0.1818 0.5878 99 D 0.1841 0.1768 0.6391 100 K 0.1099 0.1782 0.7119 101 G 0.1217 0.1059 0.7724 102 L 0.3828 0.0560 0.5612 103 K 0.5497 0.0404 0.4100 104 Y 0.7221 0.0215 0.2565 105 T 0.7476 0.0127 0.2397 106 I 0.7571 0.0137 0.2292 107 S 0.6584 0.0174 0.3242 108 L 0.4280 0.0634 0.5086