# This file is the result of combining several RDB files, specifically # T0407.t04.str2.rdb (weight 1.54425) # T0407.t04.str4.rdb (weight 0.924988) # T0407.t04.pb.rdb (weight 0.789901) # T0407.t04.bys.rdb (weight 0.748322) # T0407.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 T0407.t04.str2.rdb # ============================================ # TARGET T0407 # 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 T0407.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 2 # # ============================================ # Comments from T0407.t04.str4.rdb # ============================================ # TARGET T0407 # 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 T0407.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 2 # # ============================================ # Comments from T0407.t04.pb.rdb # ============================================ # TARGET T0407 # 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 T0407.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 2 # # ============================================ # Comments from T0407.t04.bys.rdb # ============================================ # TARGET T0407 # 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 T0407.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 2 # # ============================================ # Comments from T0407.t04.alpha.rdb # ============================================ # TARGET T0407 # 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 T0407.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 2 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 R 0.2263 0.1268 0.6469 2 S 0.1944 0.0821 0.7235 3 L 0.0373 0.5583 0.4044 4 Q 0.0393 0.6653 0.2954 5 G 0.0509 0.6716 0.2775 6 I 0.0252 0.8547 0.1201 7 R 0.0176 0.8907 0.0917 8 E 0.0164 0.8916 0.0920 9 A 0.0176 0.8688 0.1136 10 L 0.0311 0.7512 0.2177 11 D 0.0351 0.5847 0.3802 12 N 0.0522 0.3751 0.5727 13 R 0.0764 0.4014 0.5222 14 R 0.1193 0.4438 0.4369 15 T 0.1701 0.5225 0.3075 16 A 0.2046 0.5917 0.2037 17 A 0.2460 0.6009 0.1531 18 Y 0.3122 0.5423 0.1455 19 F 0.2286 0.6102 0.1611 20 H 0.1684 0.6768 0.1548 21 E 0.1999 0.6425 0.1576 22 L 0.1963 0.6070 0.1967 23 L 0.2365 0.4646 0.2988 24 I 0.2106 0.3588 0.4305 25 G 0.1528 0.2316 0.6157 26 R 0.0784 0.5035 0.4181 27 E 0.0295 0.6985 0.2719 28 D 0.0259 0.7435 0.2306 29 L 0.0342 0.6815 0.2843 30 L 0.0469 0.6543 0.2988 31 R 0.0595 0.6283 0.3122 32 P 0.0259 0.7594 0.2147 33 F 0.0289 0.7604 0.2107 34 F 0.0361 0.7627 0.2012 35 E 0.0469 0.7010 0.2520 36 K 0.0855 0.5483 0.3663 37 C 0.2356 0.2719 0.4925 38 V 0.3265 0.1541 0.5194 39 K 0.3602 0.1073 0.5325 40 I 0.2848 0.3141 0.4011 41 E 0.2499 0.3721 0.3781 42 E 0.4265 0.2405 0.3330 43 V 0.4243 0.1605 0.4153 44 S 0.3477 0.1477 0.5046 45 R 0.2671 0.2554 0.4775 46 N 0.2170 0.1847 0.5983 47 E 0.1946 0.2717 0.5337 48 Q 0.1912 0.1695 0.6393 49 G 0.2587 0.0835 0.6577 50 V 0.5049 0.0241 0.4711 51 T 0.6807 0.0163 0.3030 52 L 0.7544 0.0175 0.2281 53 S 0.7334 0.0197 0.2469 54 I 0.6346 0.0522 0.3132 55 T 0.4686 0.0859 0.4455 56 N 0.3279 0.0935 0.5786 57 V 0.1732 0.3566 0.4702 58 T 0.1398 0.4879 0.3723 59 D 0.1895 0.5726 0.2380 60 L 0.2513 0.5614 0.1873 61 V 0.2989 0.5585 0.1426 62 L 0.3881 0.4671 0.1448 63 K 0.3770 0.4338 0.1892 64 L 0.2864 0.4649 0.2487 65 K 0.2031 0.4740 0.3229 66 K 0.1788 0.4413 0.3799 67 T 0.1871 0.3192 0.4937 68 A 0.1546 0.3181 0.5273 69 H 0.1670 0.2504 0.5826 70 D 0.2137 0.2132 0.5730 71 T 0.2357 0.2980 0.4663 72 L 0.3965 0.2829 0.3206 73 L 0.6507 0.1262 0.2230 74 V 0.7369 0.0710 0.1921 75 Y 0.7357 0.0502 0.2140 76 F 0.6440 0.1181 0.2379 77 R 0.5389 0.1935 0.2677 78 D 0.4809 0.1478 0.3713 79 M 0.4894 0.1033 0.4073 80 T 0.4975 0.0754 0.4271 81 L 0.4569 0.0667 0.4764 82 K 0.3739 0.0398 0.5863 83 P 0.3230 0.1262 0.5508 84 H 0.2637 0.1308 0.6055 85 T 0.3652 0.0871 0.5477 86 R 0.4820 0.0642 0.4538 87 Y 0.6747 0.0306 0.2947 88 T 0.7405 0.0124 0.2471 89 V 0.7798 0.0113 0.2089 90 R 0.7656 0.0113 0.2231 91 I 0.7431 0.0242 0.2326 92 G 0.6246 0.0457 0.3297 93 F 0.4444 0.1320 0.4236 94 K 0.2883 0.2350 0.4766 95 Q 0.1802 0.1902 0.6296 96 G 0.1676 0.1150 0.7173 97 I 0.2895 0.0973 0.6132 98 K 0.2659 0.1003 0.6339 99 G 0.1970 0.1166 0.6864 100 G 0.1796 0.1135 0.7069 101 D 0.3004 0.0903 0.6093 102 V 0.4360 0.0960 0.4680 103 N 0.4371 0.0860 0.4769 104 F 0.5650 0.0599 0.3752 105 E 0.6162 0.0552 0.3287 106 V 0.6066 0.0489 0.3445 107 T 0.5100 0.0769 0.4131 108 N 0.5259 0.0591 0.4150 109 F 0.6664 0.0281 0.3055 110 I 0.6932 0.0269 0.2800 111 V 0.6836 0.0232 0.2932 112 A 0.4575 0.0249 0.5176 113 P 0.2746 0.1058 0.6196 114 D 0.1940 0.1600 0.6460 115 K 0.1074 0.2216 0.6709 116 G 0.1077 0.1150 0.7773 117 L 0.3380 0.0577 0.6043 118 K 0.4933 0.0472 0.4595 119 Y 0.6872 0.0251 0.2877 120 T 0.7264 0.0143 0.2593 121 I 0.7473 0.0123 0.2404 122 S 0.6527 0.0168 0.3304 123 L 0.4275 0.0584 0.5141