# This file is the result of combining several RDB files, specifically # T0475.t2k.str2.rdb (weight 1.54425) # T0475.t2k.str4.rdb (weight 0.924988) # T0475.t2k.pb.rdb (weight 0.789901) # T0475.t2k.bys.rdb (weight 0.748322) # T0475.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 T0475.t2k.str2.rdb # ============================================ # TARGET T0475 # 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 T0475.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 61.0761 # # ============================================ # Comments from T0475.t2k.str4.rdb # ============================================ # TARGET T0475 # 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 T0475.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 61.0761 # # ============================================ # Comments from T0475.t2k.pb.rdb # ============================================ # TARGET T0475 # 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 T0475.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 61.0761 # # ============================================ # Comments from T0475.t2k.bys.rdb # ============================================ # TARGET T0475 # 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 T0475.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 61.0761 # # ============================================ # Comments from T0475.t2k.alpha.rdb # ============================================ # TARGET T0475 # 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 T0475.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 61.0761 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 L 0.2088 0.1857 0.6055 2 N 0.1607 0.1561 0.6832 3 S 0.1590 0.2284 0.6126 4 E 0.1515 0.2304 0.6181 5 I 0.0933 0.4791 0.4277 6 E 0.0544 0.6909 0.2546 7 L 0.0433 0.7741 0.1826 8 P 0.0123 0.8932 0.0945 9 V 0.0091 0.9090 0.0819 10 Q 0.0084 0.9192 0.0725 11 K 0.0084 0.9172 0.0744 12 Q 0.0089 0.9101 0.0810 13 L 0.0090 0.9045 0.0865 14 E 0.0099 0.8783 0.1118 15 A 0.0182 0.8205 0.1613 16 Y 0.0371 0.6772 0.2858 17 N 0.0711 0.4957 0.4332 18 A 0.0295 0.6166 0.3539 19 R 0.0408 0.5985 0.3608 20 D 0.0653 0.6152 0.3195 21 I 0.0125 0.8288 0.1587 22 D 0.0091 0.8810 0.1099 23 A 0.0086 0.9184 0.0730 24 F 0.0085 0.9176 0.0739 25 M 0.0094 0.9045 0.0861 26 A 0.0111 0.8730 0.1159 27 W 0.0248 0.7614 0.2138 28 W 0.0722 0.5296 0.3982 29 A 0.0955 0.4826 0.4219 30 D 0.0673 0.5196 0.4131 31 D 0.1461 0.2975 0.5564 32 C 0.3766 0.2124 0.4110 33 Q 0.5069 0.1629 0.3301 34 Y 0.5825 0.1233 0.2941 35 Y 0.5529 0.0856 0.3615 36 A 0.4117 0.0598 0.5284 37 F 0.2635 0.0405 0.6960 38 P 0.1616 0.1395 0.6989 39 A 0.1092 0.2400 0.6508 40 T 0.2052 0.1865 0.6083 41 L 0.3408 0.1654 0.4938 42 L 0.4001 0.2037 0.3961 43 A 0.3477 0.2053 0.4470 44 G 0.1868 0.2294 0.5838 45 N 0.1337 0.2335 0.6329 46 A 0.0216 0.7459 0.2325 47 A 0.0121 0.8736 0.1143 48 E 0.0110 0.9068 0.0822 49 I 0.0097 0.9165 0.0738 50 R 0.0085 0.9178 0.0737 51 V 0.0087 0.9142 0.0771 52 R 0.0098 0.9037 0.0865 53 H 0.0146 0.8832 0.1022 54 I 0.0127 0.8904 0.0970 55 E 0.0159 0.8459 0.1382 56 R 0.0371 0.6754 0.2875 57 F 0.0915 0.4112 0.4972 58 K 0.1063 0.2344 0.6592 59 E 0.1725 0.1094 0.7181 60 P 0.1089 0.2895 0.6017 61 D 0.1311 0.2641 0.6047 62 L 0.1653 0.3478 0.4869 63 Y 0.2665 0.3026 0.4308 64 G 0.3660 0.2924 0.3416 65 E 0.4469 0.2730 0.2801 66 L 0.4403 0.2901 0.2695 67 L 0.3887 0.3211 0.2902 68 T 0.4357 0.2649 0.2994 69 R 0.5511 0.1492 0.2997 70 V 0.6430 0.0722 0.2847 71 I 0.5923 0.0733 0.3344 72 V 0.4334 0.0822 0.4844 73 G 0.2390 0.0736 0.6874 74 N 0.3276 0.0632 0.6092 75 V 0.6088 0.0319 0.3593 76 V 0.6911 0.0223 0.2866 77 I 0.6978 0.0242 0.2779 78 D 0.5862 0.0354 0.3785 79 H 0.5128 0.1413 0.3459 80 E 0.5665 0.1327 0.3008 81 T 0.6389 0.0801 0.2810 82 V 0.6271 0.0774 0.2955 83 T 0.5742 0.0816 0.3442 84 R 0.4565 0.1111 0.4324 85 N 0.3174 0.1040 0.5786 86 F 0.2104 0.0867 0.7029 87 P 0.0992 0.2584 0.6424 88 E 0.0866 0.1854 0.7280 89 G 0.1721 0.1219 0.7060 90 K 0.3398 0.0784 0.5818 91 G 0.4660 0.0548 0.4792 92 E 0.5965 0.0549 0.3486 93 V 0.7044 0.0253 0.2703 94 D 0.7109 0.0256 0.2635 95 V 0.8072 0.0096 0.1832 96 A 0.8012 0.0078 0.1910 97 C 0.8121 0.0072 0.1807 98 I 0.8193 0.0078 0.1730 99 Y 0.8120 0.0064 0.1816 100 E 0.7912 0.0057 0.2032 101 V 0.6981 0.0115 0.2904 102 E 0.5021 0.1293 0.3686 103 N 0.2038 0.0825 0.7137 104 G 0.0950 0.0798 0.8253 105 R 0.5083 0.0231 0.4686 106 I 0.6666 0.0203 0.3131 107 A 0.6318 0.0420 0.3262 108 K 0.7745 0.0222 0.2033 109 A 0.7596 0.0243 0.2160 110 W 0.7620 0.0315 0.2066 111 F 0.7099 0.0518 0.2383 112 K 0.5572 0.0980 0.3448 113 I 0.3145 0.0954 0.5901 114 G 0.1312 0.0860 0.7828 115 E 0.2108 0.0378 0.7514 116 P 0.2508 0.0621 0.6870 117 R 0.3695 0.1164 0.5142 118 I 0.4869 0.1015 0.4116 119 V 0.5288 0.0638 0.4074 120 S 0.3623 0.0399 0.5978 121 Q 0.2640 0.1636 0.5725 122 K 0.2140 0.1397 0.6462