# This file is the result of combining several RDB files, specifically # TR435.t2k.str2.rdb (weight 1.54425) # TR435.t2k.str4.rdb (weight 0.924988) # TR435.t2k.pb.rdb (weight 0.789901) # TR435.t2k.bys.rdb (weight 0.748322) # TR435.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 TR435.t2k.str2.rdb # ============================================ # TARGET TR435 # 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 TR435.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 87.8874 # # ============================================ # Comments from TR435.t2k.str4.rdb # ============================================ # TARGET TR435 # 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 TR435.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 87.8874 # # ============================================ # Comments from TR435.t2k.pb.rdb # ============================================ # TARGET TR435 # 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 TR435.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 87.8874 # # ============================================ # Comments from TR435.t2k.bys.rdb # ============================================ # TARGET TR435 # 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 TR435.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 87.8874 # # ============================================ # Comments from TR435.t2k.alpha.rdb # ============================================ # TARGET TR435 # 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 TR435.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 87.8874 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 S 0.1860 0.1904 0.6236 2 R 0.1335 0.3508 0.5157 3 A 0.1518 0.3299 0.5183 4 R 0.2553 0.2150 0.5297 5 L 0.2900 0.1264 0.5836 6 S 0.2802 0.0575 0.6623 7 L 0.1834 0.0595 0.7571 8 P 0.0842 0.3152 0.6006 9 K 0.0707 0.3967 0.5325 10 Q 0.1413 0.4348 0.4238 11 L 0.2753 0.3728 0.3519 12 V 0.3933 0.3032 0.3034 13 L 0.4303 0.2434 0.3263 14 R 0.3778 0.2533 0.3689 15 Q 0.3194 0.2251 0.4555 16 S 0.2901 0.1657 0.5443 17 I 0.2583 0.1602 0.5815 18 V 0.1692 0.1621 0.6687 19 G 0.1198 0.1035 0.7767 20 A 0.2940 0.1024 0.6037 21 E 0.4718 0.0754 0.4528 22 V 0.6301 0.0444 0.3255 23 G 0.7046 0.0220 0.2734 24 V 0.7413 0.0206 0.2381 25 W 0.7028 0.0306 0.2666 26 T 0.5723 0.0559 0.3718 27 G 0.3940 0.0831 0.5229 28 E 0.4832 0.0639 0.4530 29 T 0.5733 0.0402 0.3864 30 I 0.5785 0.0200 0.4015 31 P 0.4621 0.0394 0.4986 32 V 0.2639 0.2176 0.5185 33 R 0.2267 0.1644 0.6089 34 T 0.4145 0.0800 0.5055 35 C 0.5257 0.0708 0.4034 36 F 0.5063 0.0653 0.4284 37 G 0.4326 0.0566 0.5107 38 P 0.3860 0.0942 0.5198 39 L 0.4114 0.1021 0.4865 40 I 0.3858 0.1110 0.5032 41 G 0.3794 0.0868 0.5338 42 Q 0.4731 0.0871 0.4398 43 Q 0.5279 0.0765 0.3955 44 S 0.4570 0.0753 0.4676 45 H 0.3288 0.0902 0.5810 46 S 0.2059 0.2593 0.5349 47 M 0.1512 0.4480 0.4008 48 E 0.2008 0.3791 0.4201 49 V 0.1853 0.4238 0.3909 50 A 0.1219 0.5419 0.3362 51 E 0.0926 0.5861 0.3213 52 W 0.0855 0.5810 0.3334 53 T 0.0999 0.5350 0.3650 54 D 0.0835 0.5581 0.3584 55 K 0.0694 0.5713 0.3593 56 A 0.0990 0.4407 0.4603 57 V 0.1345 0.3658 0.4998 58 N 0.1747 0.2575 0.5679 59 H 0.3491 0.1749 0.4760 60 I 0.5746 0.0942 0.3312 61 W 0.7249 0.0502 0.2250 62 K 0.7601 0.0285 0.2114 63 I 0.7372 0.0313 0.2315 64 Y 0.6373 0.0530 0.3097 65 H 0.4160 0.1022 0.4818 66 N 0.1479 0.1006 0.7515 67 G 0.1091 0.0735 0.8174 68 V 0.4287 0.0316 0.5397 69 L 0.6043 0.0246 0.3711 70 E 0.7072 0.0209 0.2719 71 F 0.7881 0.0105 0.2013 72 C 0.7934 0.0073 0.1993 73 I 0.7705 0.0116 0.2179 74 I 0.6602 0.0196 0.3203 75 T 0.4017 0.0929 0.5053 76 T 0.2177 0.1183 0.6641 77 D 0.1934 0.0809 0.7257 78 E 0.0630 0.3959 0.5411 79 N 0.0846 0.3335 0.5819 80 E 0.1187 0.3974 0.4839 81 C 0.1523 0.4793 0.3684 82 N 0.2050 0.5010 0.2940 83 W 0.2360 0.5345 0.2295 84 M 0.2416 0.5486 0.2098 85 M 0.2242 0.5773 0.1986 86 F 0.2800 0.4705 0.2494 87 V 0.3215 0.3777 0.3007 88 R 0.2424 0.3621 0.3956 89 K 0.1757 0.3633 0.4611 90 A 0.1683 0.2859 0.5458 91 R 0.1595 0.1869 0.6535 92 N 0.1635 0.0863 0.7502 93 R 0.0327 0.5443 0.4230 94 E 0.0447 0.6103 0.3450 95 E 0.1070 0.5606 0.3324 96 Q 0.1961 0.4754 0.3285 97 N 0.3131 0.3173 0.3695 98 L 0.4398 0.2737 0.2865 99 V 0.5997 0.1284 0.2719 100 A 0.6459 0.0797 0.2744 101 Y 0.6193 0.0434 0.3372 102 P 0.4749 0.0789 0.4462 103 H 0.2653 0.1359 0.5988 104 D 0.1476 0.1059 0.7465 105 G 0.1325 0.0898 0.7777 106 K 0.4991 0.0190 0.4819 107 I 0.7316 0.0076 0.2609 108 F 0.7879 0.0072 0.2049 109 F 0.8015 0.0059 0.1926 110 C 0.7778 0.0104 0.2118 111 T 0.7612 0.0107 0.2281 112 S 0.6871 0.0243 0.2886 113 Q 0.5834 0.0394 0.3772 114 D 0.4904 0.0350 0.4745 115 I 0.3559 0.0199 0.6243 116 P 0.1867 0.0183 0.7950 117 P 0.1023 0.1996 0.6981 118 E 0.0594 0.1552 0.7854 119 N 0.2992 0.0874 0.6134 120 E 0.5897 0.0328 0.3774 121 L 0.7487 0.0145 0.2368 122 L 0.7847 0.0079 0.2074 123 F 0.7948 0.0101 0.1951 124 Y 0.7341 0.0196 0.2462 125 Y 0.5810 0.0433 0.3757 126 S 0.2875 0.0804 0.6321 127 R 0.0623 0.6711 0.2666 128 D 0.0258 0.8041 0.1701 129 Y 0.0218 0.8725 0.1058 130 A 0.0120 0.9016 0.0864 131 Q 0.0102 0.8927 0.0970 132 Q 0.0278 0.7789 0.1933 133 I 0.0661 0.3569 0.5770 134 G 0.0496 0.0733 0.8771 135 V 0.1783 0.0192 0.8025 136 P 0.1877 0.0454 0.7669 137 E 0.1527 0.2475 0.5998