# This file is the result of combining several RDB files, specifically # TR462.t06.str2.rdb (weight 1.54425) # TR462.t06.str4.rdb (weight 0.924988) # TR462.t06.pb.rdb (weight 0.789901) # TR462.t06.bys.rdb (weight 0.748322) # TR462.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 TR462.t06.str2.rdb # ============================================ # TARGET TR462 # 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 TR462.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 83.0494 # # ============================================ # Comments from TR462.t06.str4.rdb # ============================================ # TARGET TR462 # 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 TR462.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 83.0494 # # ============================================ # Comments from TR462.t06.pb.rdb # ============================================ # TARGET TR462 # 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 TR462.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 83.0494 # # ============================================ # Comments from TR462.t06.bys.rdb # ============================================ # TARGET TR462 # 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 TR462.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 83.0494 # # ============================================ # Comments from TR462.t06.alpha.rdb # ============================================ # TARGET TR462 # 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 TR462.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 83.0494 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.3706 0.0286 0.6008 2 K 0.2793 0.0274 0.6933 3 L 0.1805 0.3721 0.4474 4 S 0.1185 0.4990 0.3826 5 R 0.1715 0.3792 0.4493 6 L 0.3079 0.0857 0.6064 7 V 0.2257 0.0377 0.7366 8 P 0.1233 0.1772 0.6995 9 G 0.0495 0.1024 0.8481 10 V 0.2686 0.0221 0.7093 11 P 0.5206 0.0239 0.4555 12 A 0.7411 0.0109 0.2480 13 R 0.7919 0.0073 0.2008 14 I 0.7305 0.0064 0.2631 15 K 0.6865 0.0184 0.2951 16 R 0.7540 0.0108 0.2352 17 L 0.6802 0.0170 0.3029 18 E 0.5356 0.0362 0.4283 19 V 0.3357 0.1033 0.5610 20 S 0.1238 0.2228 0.6534 21 G 0.0460 0.4290 0.5251 22 E 0.0387 0.7289 0.2324 23 L 0.0271 0.8421 0.1308 24 H 0.0120 0.8984 0.0897 25 E 0.0089 0.9132 0.0779 26 K 0.0089 0.9107 0.0803 27 L 0.0130 0.8931 0.0939 28 V 0.0223 0.8369 0.1408 29 G 0.0371 0.6290 0.3339 30 M 0.0948 0.2616 0.6435 31 G 0.1494 0.1130 0.7377 32 F 0.3479 0.0491 0.6030 33 V 0.3197 0.0291 0.6512 34 P 0.1638 0.1277 0.7084 35 G 0.0790 0.0908 0.8302 36 E 0.3640 0.0312 0.6049 37 E 0.6466 0.0161 0.3373 38 I 0.7534 0.0099 0.2367 39 E 0.7689 0.0095 0.2216 40 I 0.7555 0.0076 0.2369 41 V 0.7487 0.0185 0.2328 42 Q 0.7488 0.0211 0.2301 43 V 0.6541 0.0389 0.3071 44 A 0.4390 0.0280 0.5330 45 P 0.2908 0.0983 0.6108 46 L 0.1361 0.1648 0.6991 47 G 0.0861 0.0887 0.8252 48 D 0.2305 0.0231 0.7465 49 P 0.4080 0.0353 0.5566 50 I 0.7065 0.0308 0.2626 51 V 0.7800 0.0083 0.2117 52 C 0.7991 0.0078 0.1931 53 K 0.7704 0.0070 0.2226 54 I 0.6533 0.0212 0.3255 55 G 0.3146 0.0528 0.6326 56 N 0.2288 0.0628 0.7084 57 R 0.5163 0.0388 0.4449 58 N 0.6768 0.0376 0.2857 59 I 0.7253 0.0388 0.2360 60 T 0.7119 0.0544 0.2336 61 L 0.6342 0.0920 0.2738 62 R 0.4087 0.1502 0.4411 63 K 0.1512 0.5126 0.3363 64 R 0.0858 0.5953 0.3189 65 E 0.0858 0.5513 0.3628 66 A 0.1700 0.4586 0.3713 67 D 0.1877 0.3579 0.4543 68 L 0.4430 0.1332 0.4238 69 I 0.6594 0.0263 0.3143 70 E 0.7035 0.0174 0.2792 71 V 0.7504 0.0109 0.2387 72 E 0.7206 0.0198 0.2596 73 V 0.6371 0.0272 0.3357 74 V 0.4404 0.0880 0.4715 75 G 0.2224 0.0724 0.7052 76 G 0.1955 0.0967 0.7078 77 E 0.3026 0.0961 0.6013 78 L 0.3964 0.0484 0.5552 79 P 0.4202 0.0992 0.4807 80 L 0.5356 0.1246 0.3398 81 I 0.6201 0.0810 0.2989 82 L 0.5570 0.0918 0.3512 83 A 0.3675 0.1477 0.4848 84 D 0.2078 0.2306 0.5616 85 D 0.1086 0.1519 0.7395 86 G 0.1041 0.0869 0.8089 87 T 0.3809 0.0557 0.5634 88 Y 0.5514 0.0474 0.4012 89 E 0.6154 0.0459 0.3387 90 I 0.6585 0.0456 0.2960 91 T 0.5866 0.0879 0.3255 92 K 0.5492 0.0974 0.3533 93 L 0.4788 0.1302 0.3910 94 N 0.2482 0.1415 0.6102 95 G 0.1188 0.1299 0.7513 96 G 0.1285 0.1370 0.7345 97 R 0.2260 0.2261 0.5480 98 R 0.2878 0.3479 0.3643 99 F 0.2154 0.5187 0.2659 100 L 0.1320 0.6979 0.1700 101 F 0.0997 0.7636 0.1366 102 R 0.0835 0.7746 0.1419 103 M 0.0783 0.7695 0.1522 104 K 0.0664 0.7454 0.1882 105 N 0.0687 0.6075 0.3238 106 L 0.1797 0.2907 0.5296 107 G 0.2041 0.2130 0.5829 108 I 0.2500 0.1512 0.5988 109 E 0.2072 0.2187 0.5741 110 S 0.1006 0.1584 0.7410 111 G 0.0597 0.0757 0.8646 112 K 0.3341 0.0191 0.6468 113 K 0.6764 0.0108 0.3127 114 I 0.7629 0.0079 0.2291 115 Q 0.7795 0.0073 0.2132 116 V 0.7489 0.0072 0.2439 117 S 0.6184 0.0270 0.3546 118 G 0.2975 0.0343 0.6682 119 R 0.2755 0.0459 0.6786 120 R 0.2699 0.1281 0.6019 121 Y 0.3694 0.1148 0.5159 122 Y 0.5683 0.0798 0.3519 123 I 0.5871 0.0868 0.3261 124 E 0.5448 0.0856 0.3696 125 G 0.4569 0.0993 0.4438 126 R 0.4163 0.1694 0.4143 127 E 0.4489 0.2585 0.2926 128 I 0.4166 0.2379 0.3455 129 D 0.2970 0.2698 0.4332 130 L 0.1755 0.3706 0.4538 131 G 0.1699 0.3097 0.5204 132 Y 0.1742 0.2130 0.6128 133 G 0.1531 0.1539 0.6930 134 E 0.1668 0.2779 0.5553 135 A 0.2142 0.2550 0.5308 136 T 0.3578 0.1639 0.4784 137 K 0.5842 0.0748 0.3410 138 I 0.6956 0.0399 0.2645 139 W 0.6871 0.0421 0.2709 140 V 0.6743 0.0313 0.2944 141 R 0.6386 0.0231 0.3383 142 R 0.4924 0.0225 0.4851 143 V 0.3842 0.0434 0.5724