# This file is the result of combining several RDB files, specifically # T0557.t2k.str2.rdb (weight 1.54425) # T0557.t2k.str4.rdb (weight 0.924988) # T0557.t2k.pb.rdb (weight 0.789901) # T0557.t2k.bys.rdb (weight 0.748322) # T0557.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 T0557.t2k.str2.rdb # ============================================ # TARGET T0557 # 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 T0557.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 113.814 # # ============================================ # Comments from T0557.t2k.str4.rdb # ============================================ # TARGET T0557 # 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 T0557.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 113.814 # # ============================================ # Comments from T0557.t2k.pb.rdb # ============================================ # TARGET T0557 # 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 T0557.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 113.814 # # ============================================ # Comments from T0557.t2k.bys.rdb # ============================================ # TARGET T0557 # 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 T0557.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 113.814 # # ============================================ # Comments from T0557.t2k.alpha.rdb # ============================================ # TARGET T0557 # 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 T0557.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 113.814 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.2039 0.2909 0.5052 2 R 0.1518 0.4219 0.4263 3 S 0.0857 0.6106 0.3037 4 A 0.0325 0.7602 0.2073 5 T 0.0137 0.8626 0.1237 6 D 0.0100 0.9013 0.0887 7 L 0.0097 0.9084 0.0819 8 L 0.0086 0.9143 0.0771 9 D 0.0085 0.9131 0.0784 10 E 0.0090 0.8955 0.0955 11 L 0.0161 0.8329 0.1509 12 N 0.0279 0.7187 0.2534 13 A 0.0582 0.5567 0.3851 14 V 0.0951 0.4561 0.4487 15 D 0.0773 0.5232 0.3995 16 E 0.0524 0.5862 0.3615 17 S 0.0601 0.5977 0.3422 18 A 0.0682 0.6466 0.2852 19 R 0.0787 0.7257 0.1957 20 I 0.0803 0.7925 0.1272 21 E 0.0707 0.8140 0.1153 22 A 0.0524 0.8373 0.1103 23 K 0.0473 0.8081 0.1446 24 R 0.0637 0.6795 0.2568 25 A 0.0755 0.5242 0.4003 26 S 0.0685 0.3945 0.5369 27 D 0.0744 0.2959 0.6297 28 M 0.1104 0.1873 0.7023 29 G 0.1080 0.2669 0.6251 30 K 0.0728 0.5788 0.3484 31 S 0.0976 0.5359 0.3665 32 V 0.0888 0.6429 0.2683 33 M 0.0992 0.6798 0.2210 34 E 0.1107 0.7000 0.1893 35 T 0.1851 0.6221 0.1928 36 V 0.1974 0.5978 0.2048 37 I 0.2492 0.5528 0.1980 38 A 0.2138 0.5603 0.2259 39 F 0.2360 0.3944 0.3696 40 A 0.2474 0.3045 0.4481 41 N 0.1923 0.1749 0.6329 42 E 0.1886 0.1215 0.6899 43 P 0.1166 0.1931 0.6903 44 G 0.0922 0.1270 0.7808 45 L 0.1593 0.1693 0.6714 46 D 0.1786 0.1185 0.7029 47 G 0.2541 0.0713 0.6747 48 G 0.5347 0.0234 0.4419 49 Y 0.7664 0.0070 0.2266 50 L 0.8041 0.0054 0.1905 51 L 0.7960 0.0062 0.1978 52 L 0.7496 0.0162 0.2342 53 G 0.6461 0.0196 0.3344 54 V 0.6009 0.0404 0.3587 55 D 0.4781 0.0614 0.4605 56 W 0.2648 0.3114 0.4237 57 A 0.1864 0.3290 0.4846 58 I 0.1475 0.2400 0.6125 59 N 0.1486 0.1462 0.7052 60 D 0.2406 0.1427 0.6167 61 K 0.2722 0.1053 0.6225 62 G 0.3095 0.0866 0.6039 63 D 0.3617 0.0786 0.5597 64 T 0.4567 0.0696 0.4736 65 V 0.5001 0.0672 0.4326 66 Y 0.4861 0.0618 0.4521 67 R 0.3035 0.0538 0.6426 68 P 0.2022 0.2673 0.5305 69 V 0.1174 0.1968 0.6858 70 G 0.0713 0.1186 0.8101 71 L 0.1808 0.0478 0.7714 72 P 0.1923 0.0923 0.7154 73 D 0.1703 0.0358 0.7939 74 P 0.0197 0.6714 0.3089 75 D 0.0119 0.8374 0.1506 76 K 0.0116 0.8974 0.0910 77 V 0.0105 0.9103 0.0792 78 Q 0.0095 0.9117 0.0787 79 R 0.0086 0.9130 0.0784 80 D 0.0095 0.8907 0.0997 81 L 0.0128 0.8532 0.1341 82 A 0.0185 0.8166 0.1650 83 S 0.0221 0.7771 0.2008 84 Q 0.0225 0.7800 0.1975 85 C 0.0366 0.7381 0.2253 86 A 0.0487 0.7193 0.2321 87 S 0.0598 0.6144 0.3258 88 M 0.1228 0.4089 0.4683 89 L 0.2464 0.1843 0.5693 90 N 0.2652 0.0954 0.6393 91 V 0.2728 0.1285 0.5987 92 A 0.2766 0.1111 0.6123 93 L 0.3277 0.0819 0.5903 94 R 0.2565 0.0366 0.7068 95 P 0.2083 0.1797 0.6120 96 E 0.3013 0.1020 0.5967 97 M 0.5835 0.0265 0.3900 98 Q 0.6692 0.0170 0.3138 99 L 0.7428 0.0169 0.2403 100 E 0.7236 0.0225 0.2539 101 Q 0.6597 0.0273 0.3130 102 V 0.5132 0.0515 0.4353 103 G 0.2346 0.0638 0.7016 104 G 0.1088 0.0806 0.8105 105 K 0.3918 0.0141 0.5941 106 T 0.6477 0.0083 0.3440 107 L 0.8013 0.0055 0.1932 108 L 0.8214 0.0044 0.1742 109 V 0.8232 0.0043 0.1726 110 V 0.8157 0.0050 0.1793 111 Y 0.7850 0.0055 0.2095 112 V 0.5011 0.0108 0.4881 113 P 0.2955 0.0387 0.6658 114 E 0.1905 0.2022 0.6073 115 A 0.2611 0.1424 0.5965 116 D 0.2065 0.0765 0.7170 117 V 0.0827 0.4085 0.5088 118 T 0.1174 0.3188 0.5638 119 H 0.2046 0.1600 0.6354 120 K 0.3110 0.0369 0.6521 121 P 0.4123 0.0323 0.5554 122 I 0.6260 0.0332 0.3408 123 Y 0.7113 0.0305 0.2582 124 K 0.6591 0.0513 0.2896 125 K 0.5089 0.0910 0.4001 126 A 0.3426 0.1538 0.5036 127 T 0.1499 0.1172 0.7328 128 G 0.1198 0.0808 0.7994 129 L 0.2363 0.0312 0.7325 130 P 0.2380 0.1083 0.6536 131 G 0.1888 0.1009 0.7102 132 G 0.2951 0.0604 0.6445 133 A 0.5734 0.0396 0.3871 134 Y 0.7259 0.0224 0.2518 135 R 0.7470 0.0189 0.2341 136 R 0.6694 0.0199 0.3107 137 I 0.4336 0.0566 0.5098 138 G 0.2305 0.0606 0.7089 139 S 0.1903 0.1360 0.6737 140 S 0.1993 0.1802 0.6205 141 D 0.2796 0.1695 0.5508 142 Q 0.3330 0.1913 0.4758 143 R 0.3715 0.1433 0.4852 144 C 0.3537 0.0955 0.5508 145 V 0.2344 0.0887 0.6769