# This file is the result of combining several RDB files, specifically # TR389.t2k.str2.rdb (weight 1.54425) # TR389.t2k.str4.rdb (weight 0.924988) # TR389.t2k.pb.rdb (weight 0.789901) # TR389.t2k.bys.rdb (weight 0.748322) # TR389.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 TR389.t2k.str2.rdb # ============================================ # TARGET TR389 # 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 TR389.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 372 # # ============================================ # Comments from TR389.t2k.str4.rdb # ============================================ # TARGET TR389 # 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 TR389.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 372 # # ============================================ # Comments from TR389.t2k.pb.rdb # ============================================ # TARGET TR389 # 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 TR389.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 372 # # ============================================ # Comments from TR389.t2k.bys.rdb # ============================================ # TARGET TR389 # 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 TR389.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 372 # # ============================================ # Comments from TR389.t2k.alpha.rdb # ============================================ # TARGET TR389 # 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 TR389.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 372 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.4400 0.1054 0.4546 2 I 0.3887 0.1038 0.5075 3 G 0.3443 0.1450 0.5106 4 T 0.3369 0.2358 0.4273 5 Q 0.3223 0.3113 0.3664 6 I 0.2735 0.3901 0.3364 7 V 0.1266 0.5450 0.3283 8 T 0.0236 0.8337 0.1426 9 E 0.0102 0.8860 0.1038 10 R 0.0088 0.9169 0.0743 11 L 0.0088 0.9176 0.0736 12 V 0.0084 0.9193 0.0723 13 A 0.0087 0.9144 0.0769 14 L 0.0098 0.8933 0.0969 15 L 0.0128 0.8335 0.1537 16 E 0.0307 0.6655 0.3038 17 S 0.0633 0.2833 0.6535 18 G 0.0557 0.1054 0.8389 19 T 0.1647 0.0835 0.7518 20 E 0.2123 0.0984 0.6893 21 K 0.4482 0.0389 0.5129 22 V 0.7271 0.0073 0.2656 23 L 0.8031 0.0052 0.1917 24 L 0.7917 0.0048 0.2035 25 I 0.7809 0.0091 0.2100 26 D 0.6200 0.0125 0.3675 27 S 0.3699 0.0816 0.5485 28 R 0.3161 0.0356 0.6482 29 P 0.2180 0.1010 0.6810 30 F 0.1202 0.4662 0.4136 31 V 0.1011 0.6158 0.2831 32 E 0.1358 0.5577 0.3065 33 Y 0.1577 0.5009 0.3414 34 N 0.1375 0.4010 0.4616 35 T 0.0899 0.4624 0.4477 36 S 0.1127 0.3795 0.5078 37 H 0.1841 0.2783 0.5377 38 I 0.2102 0.2665 0.5233 39 L 0.1676 0.3212 0.5112 40 E 0.1607 0.2531 0.5862 41 A 0.3085 0.2333 0.4582 42 I 0.4289 0.1516 0.4195 43 N 0.4324 0.0881 0.4796 44 I 0.3427 0.0874 0.5699 45 N 0.2120 0.0670 0.7210 46 C 0.0919 0.3842 0.5238 47 S 0.0269 0.7149 0.2582 48 K 0.0210 0.8136 0.1653 49 L 0.0157 0.8765 0.1078 50 M 0.0146 0.8833 0.1022 51 K 0.0155 0.8756 0.1089 52 R 0.0252 0.8382 0.1366 53 R 0.0325 0.7786 0.1890 54 L 0.0398 0.7021 0.2582 55 Q 0.0584 0.5431 0.3985 56 Q 0.0867 0.3972 0.5161 57 D 0.0926 0.3348 0.5726 58 K 0.0791 0.4695 0.4514 59 V 0.1464 0.4547 0.3989 60 L 0.1948 0.4529 0.3523 61 I 0.1955 0.5219 0.2826 62 T 0.2244 0.5211 0.2544 63 E 0.2658 0.4744 0.2598 64 L 0.3190 0.3696 0.3114 65 I 0.3111 0.3092 0.3798 66 Q 0.2097 0.3498 0.4405 67 H 0.1180 0.4350 0.4471 68 S 0.0830 0.4597 0.4572 69 A 0.0627 0.5496 0.3878 70 K 0.0921 0.4981 0.4097 71 H 0.1537 0.3983 0.4480 72 K 0.2213 0.2942 0.4844 73 V 0.2790 0.2570 0.4639 74 D 0.2904 0.1995 0.5101 75 I 0.2688 0.2768 0.4544 76 D 0.2238 0.2130 0.5632 77 C 0.2189 0.2298 0.5513 78 S 0.2429 0.1343 0.6228 79 Q 0.3564 0.0745 0.5691 80 K 0.5891 0.0289 0.3821 81 V 0.7596 0.0087 0.2317 82 V 0.7889 0.0068 0.2043 83 V 0.7859 0.0100 0.2042 84 Y 0.6784 0.0256 0.2960 85 D 0.4083 0.0590 0.5327 86 Q 0.1892 0.1681 0.6427 87 S 0.1718 0.1285 0.6997 88 S 0.1369 0.2771 0.5860 89 Q 0.1216 0.4503 0.4281 90 D 0.1681 0.4538 0.3780 91 V 0.1129 0.6174 0.2697 92 A 0.1124 0.5904 0.2973 93 S 0.1276 0.4872 0.3852 94 L 0.1312 0.3703 0.4985 95 S 0.1195 0.2705 0.6099 96 S 0.0406 0.5378 0.4217 97 D 0.0332 0.6288 0.3380 98 C 0.0369 0.7730 0.1901 99 F 0.0244 0.8538 0.1218 100 L 0.0170 0.8927 0.0903 101 T 0.0121 0.9144 0.0735 102 V 0.0110 0.9163 0.0727 103 L 0.0121 0.9056 0.0823 104 L 0.0144 0.8756 0.1100 105 G 0.0215 0.7984 0.1801 106 K 0.0327 0.7417 0.2257 107 L 0.0415 0.6786 0.2800 108 E 0.0480 0.5859 0.3661 109 K 0.0693 0.4051 0.5256 110 S 0.1036 0.2290 0.6674 111 F 0.1669 0.1482 0.6849 112 N 0.2086 0.1278 0.6636 113 S 0.3823 0.0714 0.5463 114 V 0.6467 0.0261 0.3272 115 H 0.7542 0.0171 0.2287 116 L 0.7519 0.0206 0.2276 117 L 0.6379 0.0539 0.3081 118 A 0.3685 0.1493 0.4822 119 G 0.1475 0.2012 0.6512 120 G 0.1064 0.3077 0.5858 121 F 0.0435 0.6748 0.2817 122 A 0.0171 0.8559 0.1270 123 E 0.0131 0.8924 0.0945 124 F 0.0125 0.8946 0.0929 125 S 0.0123 0.8731 0.1146 126 R 0.0136 0.7860 0.2004 127 C 0.0348 0.6042 0.3609 128 F 0.1246 0.2452 0.6302 129 P 0.0514 0.5040 0.4447 130 G 0.0507 0.4312 0.5181 131 L 0.1241 0.4172 0.4587 132 C 0.2121 0.1857 0.6022 133 E 0.1590 0.1970 0.6440 134 G 0.1121 0.1354 0.7526 135 K 0.1589 0.1236 0.7175