# This file is the result of combining several RDB files, specifically # T0451.t2k.str2.rdb (weight 1.54425) # T0451.t2k.str4.rdb (weight 0.924988) # T0451.t2k.pb.rdb (weight 0.789901) # T0451.t2k.bys.rdb (weight 0.748322) # T0451.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 T0451.t2k.str2.rdb # ============================================ # TARGET T0451 # 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 T0451.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 31 # # ============================================ # Comments from T0451.t2k.str4.rdb # ============================================ # TARGET T0451 # 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 T0451.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 31 # # ============================================ # Comments from T0451.t2k.pb.rdb # ============================================ # TARGET T0451 # 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 T0451.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 31 # # ============================================ # Comments from T0451.t2k.bys.rdb # ============================================ # TARGET T0451 # 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 T0451.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 31 # # ============================================ # Comments from T0451.t2k.alpha.rdb # ============================================ # TARGET T0451 # 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 T0451.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 31 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.3608 0.1468 0.4924 2 M 0.3448 0.1135 0.5417 3 T 0.2749 0.1105 0.6147 4 H 0.1815 0.2176 0.6009 5 Y 0.1493 0.2235 0.6272 6 S 0.1194 0.2491 0.6315 7 D 0.0592 0.4224 0.5183 8 N 0.0538 0.5179 0.4283 9 T 0.0546 0.6490 0.2964 10 L 0.0273 0.7985 0.1742 11 K 0.0123 0.8905 0.0972 12 V 0.0092 0.9119 0.0789 13 A 0.0086 0.9140 0.0774 14 H 0.0083 0.9199 0.0717 15 Q 0.0084 0.9188 0.0729 16 G 0.0085 0.9173 0.0742 17 F 0.0084 0.9174 0.0742 18 E 0.0084 0.9188 0.0728 19 F 0.0086 0.9150 0.0764 20 F 0.0106 0.9012 0.0882 21 T 0.0107 0.8984 0.0908 22 Q 0.0139 0.8761 0.1100 23 G 0.0251 0.8080 0.1670 24 L 0.0415 0.7340 0.2245 25 A 0.0479 0.5969 0.3552 26 T 0.0620 0.3332 0.6048 27 G 0.0452 0.2480 0.7068 28 E 0.0814 0.3990 0.5196 29 W 0.0391 0.7220 0.2389 30 Q 0.0155 0.8610 0.1234 31 K 0.0101 0.8954 0.0945 32 F 0.0102 0.8937 0.0960 33 L 0.0114 0.8811 0.1075 34 D 0.0119 0.8413 0.1468 35 M 0.0211 0.7314 0.2475 36 L 0.0779 0.4717 0.4503 37 T 0.1187 0.3596 0.5217 38 E 0.0671 0.4281 0.5048 39 D 0.1437 0.2275 0.6288 40 F 0.3751 0.1108 0.5142 41 T 0.5772 0.0681 0.3548 42 F 0.6893 0.0411 0.2696 43 W 0.6580 0.0401 0.3019 44 F 0.4732 0.0324 0.4945 45 P 0.3049 0.0970 0.5981 46 M 0.2296 0.1305 0.6399 47 G 0.1832 0.1179 0.6988 48 E 0.1750 0.2146 0.6104 49 F 0.1723 0.2397 0.5879 50 H 0.1698 0.1717 0.6584 51 G 0.1685 0.1609 0.6706 52 L 0.1480 0.2986 0.5534 53 N 0.1286 0.3207 0.5507 54 V 0.1108 0.3118 0.5774 55 G 0.0962 0.3032 0.6007 56 K 0.0169 0.7844 0.1987 57 E 0.0097 0.8896 0.1006 58 R 0.0095 0.9120 0.0785 59 A 0.0085 0.9165 0.0750 60 K 0.0084 0.9190 0.0726 61 E 0.0085 0.9163 0.0753 62 F 0.0091 0.9007 0.0902 63 F 0.0115 0.8741 0.1144 64 T 0.0126 0.8501 0.1373 65 Y 0.0279 0.7248 0.2473 66 V 0.0799 0.5997 0.3203 67 S 0.0828 0.5253 0.3919 68 E 0.0630 0.5798 0.3572 69 S 0.1004 0.4946 0.4050 70 F 0.1898 0.3549 0.4553 71 H 0.2077 0.2726 0.5196 72 T 0.1742 0.2406 0.5852 73 G 0.1766 0.1774 0.6460 74 I 0.3399 0.1493 0.5108 75 Q 0.4501 0.1042 0.4457 76 I 0.4788 0.0874 0.4339 77 S 0.4321 0.0937 0.4741 78 S 0.4227 0.0922 0.4851 79 L 0.4572 0.1252 0.4175 80 D 0.5115 0.1012 0.3873 81 R 0.5803 0.0782 0.3415 82 V 0.5051 0.0843 0.4106 83 T 0.3923 0.0886 0.5191 84 S 0.2291 0.1274 0.6435 85 N 0.1981 0.0993 0.7026 86 E 0.2853 0.0961 0.6186 87 T 0.5308 0.0270 0.4422 88 T 0.7501 0.0071 0.2428 89 V 0.8114 0.0050 0.1836 90 V 0.8220 0.0045 0.1734 91 F 0.8117 0.0055 0.1828 92 E 0.8047 0.0065 0.1887 93 F 0.7196 0.0147 0.2657 94 R 0.5408 0.0534 0.4058 95 D 0.4083 0.0905 0.5012 96 E 0.2689 0.1702 0.5609 97 G 0.3308 0.1469 0.5223 98 L 0.3906 0.1644 0.4450 99 F 0.3894 0.2015 0.4091 100 L 0.2388 0.1346 0.6266 101 G 0.1771 0.0873 0.7356 102 K 0.3405 0.0194 0.6402 103 P 0.4527 0.0329 0.5145 104 Y 0.4316 0.0718 0.4965 105 K 0.3946 0.1158 0.4896 106 N 0.4581 0.0719 0.4699 107 R 0.6472 0.0310 0.3218 108 V 0.7763 0.0084 0.2154 109 A 0.7940 0.0055 0.2005 110 V 0.8225 0.0049 0.1726 111 S 0.8197 0.0048 0.1756 112 F 0.8214 0.0050 0.1736 113 D 0.7676 0.0051 0.2273 114 V 0.6704 0.0148 0.3147 115 R 0.3721 0.0362 0.5917 116 G 0.1379 0.0744 0.7877 117 D 0.1517 0.1078 0.7404 118 K 0.5163 0.0316 0.4521 119 I 0.6366 0.0281 0.3354 120 C 0.6465 0.0387 0.3148 121 S 0.6945 0.0387 0.2667 122 Y 0.6515 0.0982 0.2503 123 R 0.6174 0.1468 0.2358 124 E 0.4900 0.2164 0.2936 125 Y 0.3660 0.1844 0.4496 126 F 0.2489 0.1402 0.6109 127 G 0.1826 0.1017 0.7156 128 S 0.1078 0.3097 0.5825 129 D 0.1100 0.2196 0.6703 130 G 0.1338 0.1684 0.6978 131 K 0.2000 0.1669 0.6331 132 S 0.2151 0.1531 0.6317 133 N 0.1676 0.1385 0.6939