# 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 83.5839 # # ============================================ # 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 83.5839 # # ============================================ # 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 83.5839 # # ============================================ # 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 83.5839 # # ============================================ # 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 83.5839 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 A 0.3326 0.1434 0.5240 2 R 0.3797 0.0857 0.5347 3 L 0.3698 0.0701 0.5601 4 S 0.3086 0.0380 0.6534 5 L 0.1861 0.0514 0.7625 6 P 0.0788 0.3197 0.6015 7 K 0.0765 0.3553 0.5682 8 Q 0.1608 0.4039 0.4354 9 L 0.2915 0.3602 0.3483 10 V 0.3982 0.3049 0.2968 11 L 0.4245 0.2579 0.3177 12 R 0.3694 0.2690 0.3616 13 Q 0.3086 0.2377 0.4538 14 S 0.2728 0.1739 0.5533 15 I 0.2439 0.1700 0.5861 16 V 0.1622 0.1646 0.6731 17 G 0.1145 0.1031 0.7824 18 A 0.2915 0.0997 0.6088 19 E 0.4713 0.0733 0.4554 20 V 0.6309 0.0434 0.3258 21 G 0.7064 0.0217 0.2719 22 V 0.7429 0.0201 0.2370 23 W 0.7039 0.0303 0.2658 24 T 0.5789 0.0549 0.3662 25 G 0.4039 0.0814 0.5147 26 E 0.4920 0.0625 0.4455 27 T 0.5774 0.0400 0.3827 28 I 0.5799 0.0198 0.4003 29 P 0.4618 0.0401 0.4981 30 V 0.2612 0.2178 0.5210 31 R 0.2236 0.1642 0.6122 32 T 0.4143 0.0790 0.5066 33 C 0.5261 0.0704 0.4035 34 F 0.5095 0.0647 0.4258 35 G 0.4373 0.0560 0.5067 36 P 0.3913 0.0929 0.5158 37 L 0.4187 0.1003 0.4809 38 I 0.3966 0.1086 0.4948 39 G 0.3933 0.0851 0.5216 40 Q 0.4844 0.0859 0.4297 41 Q 0.5379 0.0769 0.3852 42 S 0.4702 0.0745 0.4553 43 H 0.3382 0.0868 0.5750 44 S 0.2108 0.2651 0.5241 45 M 0.1469 0.4702 0.3829 46 E 0.1958 0.4085 0.3957 47 V 0.1826 0.4405 0.3769 48 A 0.1177 0.5591 0.3232 49 E 0.0858 0.6004 0.3139 50 W 0.0835 0.5674 0.3491 51 T 0.1032 0.5071 0.3896 52 D 0.0847 0.5382 0.3771 53 K 0.0706 0.5594 0.3700 54 A 0.1003 0.4388 0.4609 55 V 0.1384 0.3723 0.4893 56 N 0.1788 0.2708 0.5504 57 H 0.3437 0.1897 0.4666 58 I 0.5600 0.1080 0.3319 59 W 0.7154 0.0581 0.2265 60 K 0.7532 0.0333 0.2134 61 I 0.7292 0.0369 0.2340 62 Y 0.6288 0.0578 0.3134 63 H 0.4049 0.1106 0.4845 64 N 0.1414 0.1045 0.7540 65 G 0.1051 0.0739 0.8210 66 V 0.4245 0.0309 0.5445 67 L 0.5992 0.0244 0.3765 68 E 0.7063 0.0207 0.2730 69 F 0.7881 0.0104 0.2015 70 C 0.7933 0.0073 0.1994 71 I 0.7710 0.0114 0.2176 72 I 0.6606 0.0192 0.3201 73 T 0.4040 0.0919 0.5041 74 T 0.2208 0.1168 0.6624 75 D 0.1948 0.0780 0.7272 76 E 0.0610 0.3989 0.5401 77 N 0.0810 0.3338 0.5852 78 E 0.1213 0.3845 0.4942 79 C 0.1564 0.4612 0.3824 80 N 0.2189 0.4775 0.3036 81 W 0.2562 0.5078 0.2360 82 M 0.2646 0.5201 0.2153 83 M 0.2480 0.5490 0.2029 84 F 0.3068 0.4422 0.2510 85 V 0.3462 0.3545 0.2993 86 R 0.2556 0.3490 0.3954 87 K 0.1818 0.3597 0.4585 88 A 0.1693 0.2897 0.5410 89 R 0.1590 0.1906 0.6504 90 N 0.1630 0.0900 0.7470 91 R 0.0328 0.5429 0.4244 92 E 0.0449 0.6091 0.3460 93 E 0.1060 0.5623 0.3317 94 Q 0.1945 0.4782 0.3273 95 N 0.3112 0.3212 0.3676 96 L 0.4374 0.2781 0.2846 97 V 0.5973 0.1320 0.2707 98 A 0.6463 0.0809 0.2729 99 Y 0.6208 0.0443 0.3350 100 P 0.4774 0.0790 0.4437 101 H 0.2669 0.1363 0.5968 102 D 0.1487 0.1063 0.7450 103 G 0.1327 0.0911 0.7762 104 K 0.4982 0.0197 0.4822 105 I 0.7318 0.0076 0.2606 106 F 0.7880 0.0073 0.2046 107 F 0.8012 0.0059 0.1929 108 C 0.7779 0.0105 0.2116 109 T 0.7623 0.0107 0.2271 110 S 0.6914 0.0236 0.2851 111 Q 0.5921 0.0380 0.3699 112 D 0.4989 0.0337 0.4674 113 I 0.3593 0.0196 0.6211 114 P 0.1873 0.0182 0.7945 115 P 0.1024 0.1998 0.6978 116 E 0.0591 0.1527 0.7882 117 N 0.3028 0.0844 0.6128 118 E 0.5918 0.0310 0.3772 119 L 0.7488 0.0140 0.2372 120 L 0.7843 0.0078 0.2079 121 F 0.7947 0.0100 0.1953 122 Y 0.7339 0.0193 0.2469 123 Y 0.5819 0.0425 0.3756 124 S 0.2888 0.0788 0.6324 125 R 0.0603 0.6725 0.2671 126 D 0.0254 0.8055 0.1691 127 Y 0.0213 0.8738 0.1048 128 A 0.0118 0.9017 0.0865 129 Q 0.0102 0.8926 0.0972 130 Q 0.0278 0.7784 0.1938 131 I 0.0652 0.3528 0.5820 132 G 0.0493 0.0729 0.8778 133 V 0.1787 0.0191 0.8022 134 P 0.1855 0.0392 0.7753 135 E 0.1424 0.2517 0.6059