# This file is the result of combining several RDB files, specifically # T0467.t2k.str2.rdb (weight 1.54425) # T0467.t2k.str4.rdb (weight 0.924988) # T0467.t2k.pb.rdb (weight 0.789901) # T0467.t2k.bys.rdb (weight 0.748322) # T0467.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 T0467.t2k.str2.rdb # ============================================ # TARGET T0467 # 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 T0467.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 37.8115 # # ============================================ # Comments from T0467.t2k.str4.rdb # ============================================ # TARGET T0467 # 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 T0467.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 37.8115 # # ============================================ # Comments from T0467.t2k.pb.rdb # ============================================ # TARGET T0467 # 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 T0467.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 37.8115 # # ============================================ # Comments from T0467.t2k.bys.rdb # ============================================ # TARGET T0467 # 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 T0467.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 37.8115 # # ============================================ # Comments from T0467.t2k.alpha.rdb # ============================================ # TARGET T0467 # 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 T0467.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 37.8115 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.3294 0.1010 0.5696 2 D 0.2862 0.0980 0.6159 3 L 0.2856 0.2955 0.4189 4 N 0.3203 0.2575 0.4222 5 R 0.3560 0.1973 0.4467 6 M 0.3081 0.1531 0.5388 7 G 0.2188 0.1057 0.6755 8 K 0.2082 0.1547 0.6370 9 D 0.2489 0.1509 0.6002 10 E 0.3933 0.1131 0.4936 11 Y 0.5414 0.0443 0.4142 12 Y 0.6644 0.0261 0.3094 13 V 0.7409 0.0156 0.2435 14 Q 0.7595 0.0108 0.2297 15 I 0.7541 0.0106 0.2353 16 T 0.6664 0.0204 0.3132 17 V 0.5474 0.0623 0.3903 18 D 0.3283 0.0595 0.6122 19 G 0.3014 0.0611 0.6375 20 K 0.5742 0.0269 0.3989 21 E 0.6904 0.0171 0.2925 22 V 0.7320 0.0222 0.2458 23 H 0.7133 0.0272 0.2595 24 S 0.6252 0.0421 0.3327 25 K 0.4642 0.0875 0.4484 26 A 0.2622 0.1690 0.5688 27 D 0.1786 0.2104 0.6110 28 N 0.1427 0.1308 0.7265 29 G 0.1652 0.0870 0.7478 30 Q 0.3642 0.0650 0.5708 31 K 0.4469 0.0729 0.4802 32 Y 0.4622 0.0726 0.4652 33 K 0.4664 0.0744 0.4592 34 D 0.5981 0.0391 0.3628 35 Y 0.6952 0.0159 0.2889 36 E 0.7488 0.0112 0.2400 37 Y 0.7843 0.0097 0.2060 38 K 0.7756 0.0082 0.2162 39 L 0.7345 0.0151 0.2504 40 T 0.6717 0.0321 0.2962 41 G 0.6432 0.0381 0.3188 42 F 0.6138 0.0434 0.3428 43 D 0.4335 0.0312 0.5354 44 K 0.1557 0.3382 0.5061 45 D 0.0756 0.1748 0.7496 46 G 0.1091 0.0777 0.8132 47 K 0.4249 0.0195 0.5557 48 E 0.6590 0.0139 0.3271 49 K 0.6850 0.0186 0.2964 50 E 0.7561 0.0073 0.2366 51 L 0.7874 0.0063 0.2063 52 E 0.7810 0.0054 0.2137 53 F 0.7434 0.0108 0.2458 54 T 0.5309 0.0303 0.4389 55 A 0.4048 0.1485 0.4468 56 Q 0.2398 0.2505 0.5097 57 K 0.1985 0.3237 0.4778 58 N 0.1980 0.3029 0.4991 59 L 0.2499 0.2730 0.4771 60 R 0.2360 0.2343 0.5297 61 K 0.1372 0.4018 0.4610 62 E 0.1434 0.3159 0.5408 63 A 0.3511 0.2077 0.4413 64 F 0.5846 0.1104 0.3050 65 L 0.7436 0.0452 0.2112 66 R 0.7624 0.0227 0.2149 67 V 0.7752 0.0150 0.2098 68 Y 0.7520 0.0165 0.2315 69 H 0.6606 0.0304 0.3090 70 S 0.3643 0.0844 0.5513 71 D 0.1928 0.1257 0.6816 72 K 0.1837 0.1930 0.6233 73 K 0.1988 0.1283 0.6729 74 G 0.2697 0.0613 0.6690 75 V 0.4466 0.0335 0.5199 76 S 0.4742 0.0348 0.4910 77 A 0.4320 0.0652 0.5028 78 W 0.2446 0.4275 0.3279 79 E 0.2651 0.4611 0.2738 80 E 0.3397 0.3568 0.3036 81 V 0.3830 0.2820 0.3350 82 K 0.2311 0.2044 0.5645 83 K 0.0413 0.6382 0.3204 84 D 0.0278 0.5657 0.4065 85 E 0.0657 0.3993 0.5350 86 L 0.1429 0.2217 0.6354 87 P 0.1038 0.3832 0.5131 88 A 0.0111 0.7992 0.1897 89 K 0.0109 0.8896 0.0995 90 V 0.0116 0.8959 0.0925 91 K 0.0099 0.9064 0.0837 92 E 0.0109 0.8920 0.0971 93 K 0.0269 0.7469 0.2261 94 L 0.0901 0.4090 0.5008 95 G 0.1052 0.1061 0.7887 96 V 0.2456 0.0543 0.7001 97 K 0.2435 0.0674 0.6891