# This file is the result of combining several RDB files, specifically # TR435.t06.str2.rdb (weight 1.54425) # TR435.t06.str4.rdb (weight 0.924988) # TR435.t06.pb.rdb (weight 0.789901) # TR435.t06.bys.rdb (weight 0.748322) # TR435.t06.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 TR435.t06.str2.rdb # ============================================ # TARGET TR435 # Using neural net dunbrack-40pc-3157-t06-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 TR435.t06-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 852 # # ============================================ # Comments from TR435.t06.str4.rdb # ============================================ # TARGET TR435 # Using neural net dunbrack-40pc-3157-t06-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 TR435.t06-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 852 # # ============================================ # Comments from TR435.t06.pb.rdb # ============================================ # TARGET TR435 # Using neural net dunbrack-40pc-3157-t06-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 TR435.t06-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 852 # # ============================================ # Comments from TR435.t06.bys.rdb # ============================================ # TARGET TR435 # Using neural net dunbrack-40pc-3157-t06-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 TR435.t06-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 852 # # ============================================ # Comments from TR435.t06.alpha.rdb # ============================================ # TARGET TR435 # Using neural net dunbrack-40pc-3157-t06-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 TR435.t06-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 852 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 S 0.1984 0.2929 0.5087 2 R 0.2197 0.3821 0.3983 3 A 0.2132 0.4383 0.3486 4 R 0.2112 0.4105 0.3783 5 L 0.2391 0.2650 0.4959 6 S 0.2235 0.1479 0.6286 7 L 0.2592 0.0469 0.6939 8 P 0.2028 0.0485 0.7487 9 K 0.1640 0.2293 0.6067 10 Q 0.2820 0.1456 0.5725 11 L 0.5817 0.0311 0.3872 12 V 0.7063 0.0161 0.2775 13 L 0.7010 0.0136 0.2854 14 R 0.6761 0.0230 0.3009 15 Q 0.5914 0.0388 0.3699 16 S 0.4528 0.0583 0.4889 17 I 0.3647 0.1158 0.5195 18 V 0.2016 0.1500 0.6483 19 G 0.1388 0.1179 0.7433 20 A 0.1919 0.1594 0.6488 21 E 0.2427 0.1256 0.6317 22 V 0.4458 0.0758 0.4784 23 G 0.5613 0.0549 0.3839 24 V 0.6995 0.0419 0.2585 25 W 0.6824 0.0526 0.2650 26 T 0.5598 0.0757 0.3645 27 G 0.4019 0.1003 0.4979 28 E 0.4774 0.0815 0.4411 29 T 0.4185 0.0837 0.4979 30 I 0.3760 0.0320 0.5920 31 P 0.2332 0.0586 0.7083 32 V 0.1065 0.2348 0.6587 33 R 0.0895 0.1341 0.7764 34 T 0.3845 0.0481 0.5674 35 C 0.6039 0.0350 0.3611 36 F 0.6114 0.0356 0.3530 37 G 0.5524 0.0320 0.4156 38 P 0.4519 0.0957 0.4524 39 L 0.4057 0.1238 0.4704 40 I 0.3064 0.1440 0.5496 41 G 0.2583 0.1010 0.6407 42 Q 0.4498 0.0913 0.4589 43 Q 0.5326 0.0669 0.4005 44 S 0.4215 0.0731 0.5053 45 H 0.2750 0.0530 0.6720 46 S 0.0832 0.5257 0.3912 47 M 0.0492 0.7217 0.2290 48 E 0.0750 0.7360 0.1890 49 V 0.0780 0.7373 0.1847 50 A 0.0574 0.7368 0.2057 51 E 0.0736 0.6546 0.2718 52 W 0.1143 0.5038 0.3819 53 T 0.1363 0.3749 0.4888 54 D 0.1179 0.3704 0.5117 55 K 0.0682 0.4813 0.4505 56 A 0.0925 0.4034 0.5041 57 V 0.1496 0.3680 0.4824 58 N 0.2046 0.2712 0.5241 59 H 0.3581 0.1957 0.4462 60 I 0.5227 0.1492 0.3281 61 W 0.6454 0.1089 0.2457 62 K 0.7469 0.0597 0.1933 63 I 0.7421 0.0546 0.2033 64 Y 0.6755 0.0697 0.2548 65 H 0.5821 0.0849 0.3330 66 N 0.2662 0.0973 0.6365 67 G 0.1382 0.0703 0.7914 68 V 0.3199 0.0469 0.6332 69 L 0.4548 0.0506 0.4946 70 E 0.6751 0.0239 0.3011 71 F 0.7803 0.0091 0.2106 72 C 0.7980 0.0064 0.1955 73 I 0.7894 0.0075 0.2031 74 I 0.6608 0.0150 0.3242 75 T 0.4217 0.0808 0.4976 76 T 0.2712 0.0930 0.6358 77 D 0.2053 0.1103 0.6845 78 E 0.0734 0.3655 0.5611 79 N 0.0837 0.3031 0.6132 80 E 0.1030 0.3105 0.5865 81 C 0.1362 0.3582 0.5056 82 N 0.1380 0.4791 0.3829 83 W 0.0746 0.7359 0.1896 84 M 0.0771 0.7849 0.1379 85 M 0.0916 0.7897 0.1187 86 F 0.1129 0.7503 0.1368 87 V 0.1605 0.6259 0.2136 88 R 0.1342 0.5094 0.3564 89 K 0.1176 0.3502 0.5321 90 A 0.1421 0.2383 0.6197 91 R 0.1566 0.1652 0.6782 92 N 0.1767 0.0813 0.7420 93 R 0.0327 0.4927 0.4745 94 E 0.0588 0.3808 0.5604 95 E 0.1881 0.3379 0.4740 96 Q 0.3762 0.1905 0.4332 97 N 0.5228 0.1069 0.3703 98 L 0.6664 0.0495 0.2841 99 V 0.7376 0.0232 0.2393 100 A 0.7381 0.0154 0.2464 101 Y 0.6840 0.0148 0.3012 102 P 0.5026 0.0675 0.4299 103 H 0.2046 0.1511 0.6443 104 D 0.1323 0.0899 0.7778 105 G 0.1801 0.0626 0.7572 106 K 0.5818 0.0195 0.3987 107 I 0.7428 0.0069 0.2503 108 F 0.8105 0.0062 0.1833 109 F 0.8198 0.0049 0.1753 110 C 0.7973 0.0084 0.1944 111 T 0.7551 0.0148 0.2301 112 S 0.5847 0.0574 0.3579 113 Q 0.4444 0.1022 0.4534 114 D 0.2676 0.1014 0.6311 115 I 0.2917 0.0226 0.6857 116 P 0.1653 0.0157 0.8190 117 P 0.0740 0.3067 0.6192 118 E 0.0520 0.1597 0.7883 119 N 0.3194 0.0722 0.6084 120 E 0.6626 0.0292 0.3082 121 L 0.7679 0.0228 0.2093 122 L 0.8001 0.0106 0.1894 123 F 0.7668 0.0164 0.2168 124 Y 0.6305 0.0441 0.3254 125 Y 0.4241 0.0989 0.4770 126 S 0.2433 0.1370 0.6197 127 R 0.1217 0.3621 0.5162 128 D 0.0974 0.4630 0.4396 129 Y 0.0665 0.6590 0.2744 130 A 0.0407 0.7423 0.2169 131 Q 0.0431 0.7225 0.2344 132 Q 0.0605 0.5924 0.3472 133 I 0.1067 0.2641 0.6292 134 G 0.0733 0.1214 0.8053 135 V 0.2016 0.0274 0.7711 136 P 0.1742 0.0866 0.7392 137 E 0.1803 0.1245 0.6951