# This file is the result of combining several RDB files, specifically # T0411.t04.str2.rdb (weight 1.54425) # T0411.t04.str4.rdb (weight 0.924988) # T0411.t04.pb.rdb (weight 0.789901) # T0411.t04.bys.rdb (weight 0.748322) # T0411.t04.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 T0411.t04.str2.rdb # ============================================ # TARGET T0411 # Using neural net dunbrack-40pc-3157-t04-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 T0411.t04-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 2643 # # ============================================ # Comments from T0411.t04.str4.rdb # ============================================ # TARGET T0411 # Using neural net dunbrack-40pc-3157-t04-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 T0411.t04-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 2643 # # ============================================ # Comments from T0411.t04.pb.rdb # ============================================ # TARGET T0411 # Using neural net dunbrack-40pc-3157-t04-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 T0411.t04-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 2643 # # ============================================ # Comments from T0411.t04.bys.rdb # ============================================ # TARGET T0411 # Using neural net dunbrack-40pc-3157-t04-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 T0411.t04-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 2643 # # ============================================ # Comments from T0411.t04.alpha.rdb # ============================================ # TARGET T0411 # Using neural net dunbrack-40pc-3157-t04-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 T0411.t04-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 2643 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.2300 0.2292 0.5408 2 W 0.2078 0.3062 0.4861 3 K 0.1981 0.4456 0.3563 4 A 0.2587 0.4285 0.3127 5 V 0.3430 0.3503 0.3067 6 M 0.3289 0.3558 0.3153 7 N 0.2753 0.3521 0.3726 8 A 0.2156 0.3656 0.4189 9 W 0.1598 0.3438 0.4964 10 N 0.1375 0.2095 0.6529 11 G 0.1271 0.1294 0.7435 12 T 0.1792 0.1612 0.6596 13 E 0.1578 0.3109 0.5313 14 S 0.1603 0.3344 0.5053 15 Q 0.1976 0.2552 0.5472 16 S 0.2102 0.1565 0.6332 17 K 0.1336 0.3595 0.5070 18 N 0.1557 0.2456 0.5987 19 V 0.1835 0.2703 0.5462 20 S 0.1702 0.2136 0.6162 21 N 0.1821 0.2021 0.6158 22 I 0.2664 0.1438 0.5898 23 Q 0.3707 0.1395 0.4898 24 S 0.4914 0.0579 0.4507 25 Y 0.4092 0.0270 0.5638 26 S 0.1918 0.0138 0.7944 27 F 0.0180 0.7153 0.2667 28 E 0.0098 0.8626 0.1276 29 D 0.0094 0.9069 0.0838 30 M 0.0088 0.9075 0.0837 31 K 0.0086 0.9076 0.0838 32 R 0.0087 0.8904 0.1010 33 I 0.0112 0.8513 0.1375 34 V 0.0272 0.6946 0.2783 35 G 0.0329 0.4837 0.4834 36 K 0.0736 0.2882 0.6382 37 H 0.1162 0.1531 0.7308 38 D 0.2091 0.0449 0.7460 39 P 0.1123 0.2820 0.6057 40 N 0.1295 0.1290 0.7414 41 V 0.4641 0.0117 0.5243 42 V 0.6952 0.0142 0.2906 43 L 0.7786 0.0051 0.2163 44 V 0.7620 0.0126 0.2254 45 D 0.7144 0.0090 0.2765 46 V 0.5364 0.0432 0.4204 47 R 0.3410 0.0422 0.6168 48 E 0.2233 0.0205 0.7561 49 P 0.0796 0.4068 0.5137 50 S 0.0527 0.5658 0.3815 51 E 0.0917 0.6075 0.3009 52 Y 0.1737 0.4841 0.3423 53 S 0.2163 0.4301 0.3536 54 I 0.2960 0.3113 0.3927 55 V 0.3602 0.1582 0.4816 56 H 0.3957 0.0852 0.5191 57 I 0.3338 0.0447 0.6215 58 P 0.1976 0.1878 0.6146 59 A 0.1622 0.1549 0.6830 60 S 0.3329 0.1298 0.5373 61 I 0.5130 0.0932 0.3938 62 N 0.5179 0.0459 0.4363 63 V 0.4442 0.0369 0.5189 64 P 0.2706 0.0409 0.6885 65 Y 0.1367 0.3909 0.4724 66 R 0.0994 0.3665 0.5340 67 S 0.1332 0.2909 0.5760 68 H 0.1894 0.1372 0.6734 69 P 0.0719 0.4325 0.4956 70 D 0.0690 0.4361 0.4949 71 A 0.0713 0.5042 0.4246 72 F 0.1089 0.3136 0.5774 73 A 0.1539 0.2069 0.6392 74 L 0.1852 0.1095 0.7053 75 D 0.1751 0.0241 0.8008 76 P 0.0141 0.7317 0.2542 77 L 0.0100 0.8448 0.1451 78 E 0.0097 0.8938 0.0965 79 F 0.0098 0.8933 0.0969 80 E 0.0099 0.8993 0.0908 81 K 0.0102 0.8770 0.1127 82 Q 0.0171 0.7822 0.2007 83 I 0.0639 0.4912 0.4448 84 G 0.0573 0.2466 0.6961 85 I 0.1542 0.1140 0.7318 86 P 0.1497 0.1368 0.7135 87 K 0.2220 0.0602 0.7178 88 P 0.1903 0.1291 0.6805 89 D 0.2070 0.0669 0.7261 90 S 0.0870 0.3171 0.5958 91 A 0.1045 0.1743 0.7211 92 K 0.3243 0.0344 0.6413 93 E 0.5652 0.0144 0.4204 94 L 0.7792 0.0073 0.2135 95 I 0.8102 0.0058 0.1841 96 F 0.8159 0.0048 0.1793 97 Y 0.7773 0.0073 0.2154 98 C 0.5278 0.0258 0.4464 99 A 0.2353 0.1717 0.5930 100 S 0.1383 0.1598 0.7019 101 G 0.1026 0.2037 0.6938 102 K 0.0976 0.4986 0.4038 103 R 0.0718 0.6718 0.2564 104 G 0.0197 0.8620 0.1183 105 G 0.0091 0.9143 0.0766 106 E 0.0085 0.9211 0.0704 107 A 0.0083 0.9231 0.0685 108 Q 0.0083 0.9234 0.0683 109 K 0.0083 0.9241 0.0676 110 V 0.0083 0.9226 0.0691 111 A 0.0085 0.9160 0.0755 112 S 0.0091 0.8992 0.0917 113 S 0.0145 0.7974 0.1881 114 H 0.0555 0.2597 0.6848 115 G 0.0519 0.0935 0.8546 116 Y 0.1707 0.0790 0.7503 117 S 0.1931 0.1509 0.6560 118 N 0.2602 0.1155 0.6243 119 T 0.4242 0.0659 0.5099 120 S 0.5746 0.0690 0.3564 121 L 0.6081 0.0603 0.3316 122 Y 0.3884 0.0822 0.5294 123 P 0.1945 0.1939 0.6116 124 G 0.1417 0.2127 0.6455 125 S 0.1644 0.3156 0.5200 126 M 0.0645 0.6042 0.3314 127 N 0.0405 0.7506 0.2089 128 D 0.0274 0.8449 0.1278 129 W 0.0202 0.8503 0.1295 130 V 0.0282 0.8236 0.1483 131 S 0.0444 0.6757 0.2799 132 H 0.0757 0.3371 0.5871 133 G 0.0793 0.1230 0.7977 134 G 0.1232 0.0797 0.7971 135 D 0.1769 0.0982 0.7250 136 K 0.2395 0.1654 0.5951 137 L 0.2935 0.1454 0.5611 138 D 0.2487 0.1155 0.6358 139 L 0.2215 0.1722 0.6063