# 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 2637 # # ============================================ # 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 2637 # # ============================================ # 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 2637 # # ============================================ # 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 2637 # # ============================================ # 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 2637 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.2570 0.2099 0.5331 2 W 0.2246 0.2942 0.4812 3 K 0.1950 0.4525 0.3525 4 A 0.2388 0.4456 0.3156 5 V 0.3133 0.3657 0.3210 6 M 0.3351 0.3468 0.3181 7 N 0.3246 0.3226 0.3528 8 A 0.2765 0.3126 0.4109 9 W 0.2095 0.2738 0.5167 10 N 0.1570 0.1935 0.6495 11 G 0.1315 0.1282 0.7402 12 T 0.1775 0.1675 0.6550 13 E 0.1655 0.2985 0.5360 14 S 0.1739 0.3111 0.5150 15 Q 0.2131 0.2499 0.5369 16 S 0.2220 0.1549 0.6231 17 K 0.1411 0.3568 0.5020 18 N 0.1619 0.2430 0.5951 19 V 0.1862 0.2670 0.5468 20 S 0.1711 0.2129 0.6160 21 N 0.1818 0.2047 0.6135 22 I 0.2652 0.1489 0.5859 23 Q 0.3647 0.1457 0.4897 24 S 0.4865 0.0598 0.4538 25 Y 0.4068 0.0272 0.5660 26 S 0.1909 0.0138 0.7953 27 F 0.0179 0.7153 0.2668 28 E 0.0097 0.8623 0.1280 29 D 0.0094 0.9068 0.0838 30 M 0.0088 0.9070 0.0843 31 K 0.0086 0.9071 0.0843 32 R 0.0087 0.8891 0.1022 33 I 0.0112 0.8495 0.1393 34 V 0.0271 0.6901 0.2828 35 G 0.0334 0.4763 0.4903 36 K 0.0753 0.2822 0.6425 37 H 0.1169 0.1515 0.7316 38 D 0.2099 0.0443 0.7459 39 P 0.1148 0.2787 0.6065 40 N 0.1307 0.1281 0.7412 41 V 0.4665 0.0116 0.5219 42 V 0.6955 0.0141 0.2903 43 L 0.7790 0.0051 0.2159 44 V 0.7629 0.0124 0.2247 45 D 0.7149 0.0090 0.2761 46 V 0.5378 0.0428 0.4194 47 R 0.3416 0.0421 0.6162 48 E 0.2239 0.0205 0.7556 49 P 0.0809 0.4004 0.5187 50 S 0.0537 0.5632 0.3831 51 E 0.0920 0.6067 0.3013 52 Y 0.1734 0.4851 0.3415 53 S 0.2170 0.4304 0.3525 54 I 0.2987 0.3099 0.3914 55 V 0.3619 0.1579 0.4802 56 H 0.3961 0.0848 0.5192 57 I 0.3331 0.0449 0.6220 58 P 0.1959 0.1882 0.6159 59 A 0.1589 0.1538 0.6873 60 S 0.3320 0.1279 0.5402 61 I 0.5143 0.0921 0.3936 62 N 0.5207 0.0450 0.4342 63 V 0.4465 0.0365 0.5170 64 P 0.2716 0.0401 0.6883 65 Y 0.1370 0.3903 0.4727 66 R 0.0990 0.3663 0.5348 67 S 0.1335 0.2888 0.5777 68 H 0.1902 0.1352 0.6746 69 P 0.0729 0.4281 0.4990 70 D 0.0701 0.4309 0.4990 71 A 0.0722 0.4990 0.4289 72 F 0.1111 0.3112 0.5777 73 A 0.1553 0.2059 0.6388 74 L 0.1864 0.1091 0.7046 75 D 0.1753 0.0238 0.8009 76 P 0.0142 0.7318 0.2541 77 L 0.0100 0.8450 0.1449 78 E 0.0097 0.8928 0.0975 79 F 0.0100 0.8926 0.0974 80 E 0.0099 0.8988 0.0913 81 K 0.0103 0.8763 0.1135 82 Q 0.0174 0.7821 0.2005 83 I 0.0643 0.4915 0.4442 84 G 0.0574 0.2454 0.6972 85 I 0.1543 0.1151 0.7306 86 P 0.1506 0.1353 0.7140 87 K 0.2233 0.0601 0.7166 88 P 0.1914 0.1274 0.6812 89 D 0.2080 0.0650 0.7269 90 S 0.0853 0.3190 0.5957 91 A 0.1034 0.1753 0.7213 92 K 0.3228 0.0348 0.6425 93 E 0.5637 0.0144 0.4219 94 L 0.7785 0.0073 0.2142 95 I 0.8100 0.0059 0.1841 96 F 0.8160 0.0048 0.1792 97 Y 0.7776 0.0073 0.2152 98 C 0.5285 0.0257 0.4458 99 A 0.2357 0.1740 0.5902 100 S 0.1381 0.1626 0.6993 101 G 0.1024 0.2087 0.6889 102 K 0.0965 0.5052 0.3983 103 R 0.0709 0.6757 0.2534 104 G 0.0194 0.8635 0.1172 105 G 0.0091 0.9147 0.0762 106 E 0.0085 0.9212 0.0703 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 0.9162 0.0754 112 S 0.0091 0.8993 0.0916 113 S 0.0144 0.7976 0.1880 114 H 0.0555 0.2585 0.6860 115 G 0.0518 0.0928 0.8554 116 Y 0.1697 0.0787 0.7516 117 S 0.1927 0.1510 0.6563 118 N 0.2591 0.1155 0.6254 119 T 0.4214 0.0658 0.5127 120 S 0.5731 0.0692 0.3577 121 L 0.6080 0.0599 0.3320 122 Y 0.3884 0.0830 0.5286 123 P 0.1947 0.1946 0.6106 124 G 0.1415 0.2143 0.6442 125 S 0.1646 0.3175 0.5179 126 M 0.0651 0.6051 0.3298 127 N 0.0417 0.7483 0.2100 128 D 0.0292 0.8410 0.1298 129 W 0.0222 0.8481 0.1297 130 V 0.0327 0.8137 0.1536 131 S 0.0482 0.6662 0.2856 132 H 0.0799 0.3213 0.5988 133 G 0.0830 0.1089 0.8081 134 G 0.1328 0.0816 0.7856 135 D 0.2138 0.0915 0.6947 136 K 0.2833 0.1036 0.6131 137 L 0.2784 0.1287 0.5929 138 D 0.2114 0.1300 0.6587 139 L 0.2087 0.1804 0.6109