# This file is the result of combining several RDB files, specifically # T0523.t06.str2.rdb (weight 1.54425) # T0523.t06.str4.rdb (weight 0.924988) # T0523.t06.pb.rdb (weight 0.789901) # T0523.t06.bys.rdb (weight 0.748322) # T0523.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 T0523.t06.str2.rdb # ============================================ # TARGET T0523 # 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 T0523.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 26209 # # ============================================ # Comments from T0523.t06.str4.rdb # ============================================ # TARGET T0523 # 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 T0523.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 26209 # # ============================================ # Comments from T0523.t06.pb.rdb # ============================================ # TARGET T0523 # 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 T0523.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 26209 # # ============================================ # Comments from T0523.t06.bys.rdb # ============================================ # TARGET T0523 # 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 T0523.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 26209 # # ============================================ # Comments from T0523.t06.alpha.rdb # ============================================ # TARGET T0523 # 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 T0523.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 26209 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 P 0.1632 0.0728 0.7640 2 A 0.0395 0.5553 0.4052 3 I 0.0236 0.7253 0.2511 4 D 0.0296 0.7766 0.1938 5 Y 0.0166 0.8528 0.1305 6 K 0.0099 0.8983 0.0918 7 T 0.0117 0.9005 0.0878 8 A 0.0142 0.8901 0.0957 9 F 0.0181 0.8538 0.1281 10 H 0.0321 0.6976 0.2703 11 L 0.0729 0.4290 0.4981 12 A 0.1745 0.1571 0.6684 13 P 0.1635 0.2168 0.6197 14 I 0.3162 0.1383 0.5454 15 G 0.6277 0.0514 0.3209 16 L 0.7643 0.0134 0.2223 17 V 0.8006 0.0074 0.1920 18 L 0.7693 0.0100 0.2207 19 S 0.6567 0.0232 0.3201 20 R 0.3535 0.1121 0.5344 21 D 0.1603 0.1116 0.7281 22 R 0.2238 0.0914 0.6849 23 V 0.4633 0.0858 0.4510 24 I 0.5019 0.1644 0.3337 25 E 0.3402 0.3598 0.3000 26 D 0.2799 0.3794 0.3407 27 C 0.1992 0.3918 0.4090 28 N 0.1684 0.3766 0.4550 29 D 0.0114 0.7650 0.2237 30 E 0.0092 0.8730 0.1179 31 L 0.0086 0.9195 0.0719 32 A 0.0084 0.9137 0.0779 33 A 0.0087 0.8977 0.0936 34 I 0.0134 0.7795 0.2071 35 F 0.0531 0.3657 0.5812 36 R 0.0416 0.1485 0.8099 37 C 0.1645 0.0475 0.7881 38 A 0.1661 0.0284 0.8055 39 R 0.0191 0.6943 0.2867 40 A 0.0159 0.7723 0.2118 41 D 0.0336 0.7557 0.2108 42 L 0.0887 0.5748 0.3365 43 I 0.1148 0.3338 0.5515 44 G 0.0859 0.1724 0.7417 45 R 0.2004 0.0805 0.7191 46 S 0.1893 0.0706 0.7400 47 F 0.0796 0.4740 0.4464 48 E 0.0667 0.5754 0.3578 49 V 0.1234 0.4919 0.3847 50 L 0.2237 0.2118 0.5645 51 Y 0.2276 0.1044 0.6681 52 P 0.2173 0.0740 0.7088 53 S 0.1726 0.0327 0.7947 54 S 0.0184 0.6621 0.3195 55 D 0.0175 0.6479 0.3346 56 E 0.0319 0.7280 0.2401 57 F 0.0209 0.8421 0.1369 58 E 0.0111 0.8911 0.0978 59 R 0.0125 0.8812 0.1064 60 I 0.0178 0.8585 0.1237 61 G 0.0118 0.8774 0.1108 62 E 0.0104 0.8826 0.1069 63 R 0.0152 0.8422 0.1426 64 I 0.0211 0.8165 0.1625 65 S 0.0142 0.8638 0.1220 66 P 0.0129 0.8850 0.1021 67 V 0.0168 0.8738 0.1094 68 M 0.0380 0.8236 0.1384 69 I 0.0689 0.6502 0.2809 70 A 0.0754 0.3549 0.5697 71 H 0.0823 0.1424 0.7753 72 G 0.1735 0.0840 0.7425 73 S 0.3096 0.0795 0.6109 74 Y 0.3358 0.0862 0.5780 75 A 0.3993 0.1163 0.4844 76 D 0.4762 0.1403 0.3834 77 D 0.6170 0.0889 0.2941 78 R 0.7319 0.0424 0.2257 79 I 0.7451 0.0355 0.2195 80 M 0.7461 0.0364 0.2175 81 K 0.7122 0.0454 0.2424 82 R 0.6224 0.0326 0.3450 83 A 0.2153 0.2041 0.5807 84 G 0.0806 0.1321 0.7872 85 G 0.0926 0.0537 0.8538 86 E 0.5220 0.0203 0.4577 87 L 0.6905 0.0100 0.2994 88 F 0.7607 0.0132 0.2262 89 W 0.7816 0.0064 0.2120 90 C 0.8040 0.0072 0.1888 91 H 0.8073 0.0061 0.1866 92 V 0.7847 0.0088 0.2065 93 T 0.7126 0.0217 0.2657 94 G 0.6401 0.0229 0.3370 95 R 0.6516 0.0225 0.3259 96 A 0.5587 0.0435 0.3977 97 L 0.3919 0.0814 0.5267 98 D 0.2357 0.0575 0.7068 99 R 0.0521 0.3738 0.5741 100 T 0.0883 0.2013 0.7104 101 A 0.1729 0.0856 0.7415 102 P 0.2770 0.0849 0.6381 103 L 0.4254 0.1260 0.4486 104 A 0.4740 0.1138 0.4122 105 A 0.6770 0.0529 0.2702 106 G 0.7263 0.0329 0.2408 107 V 0.7758 0.0241 0.2001 108 W 0.7731 0.0219 0.2050 109 T 0.7186 0.0384 0.2430 110 F 0.5562 0.1366 0.3072 111 E 0.3287 0.2524 0.4189 112 D 0.2115 0.2484 0.5402 113 L 0.0994 0.4370 0.4637 114 S 0.0837 0.5020 0.4143 115 A 0.0480 0.7307 0.2213 116 T 0.0470 0.7353 0.2177 117 R 0.0669 0.7203 0.2128 118 R 0.1079 0.6317 0.2603 119 V 0.1361 0.4804 0.3835 120 A 0.2016 0.2999 0.4985