# This file is the result of combining several RDB files, specifically # T0401.t2k.str2.rdb (weight 1.54425) # T0401.t2k.str4.rdb (weight 0.924988) # T0401.t2k.pb.rdb (weight 0.789901) # T0401.t2k.bys.rdb (weight 0.748322) # T0401.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 T0401.t2k.str2.rdb # ============================================ # TARGET T0401 # 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 T0401.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 # # ============================================ # Comments from T0401.t2k.str4.rdb # ============================================ # TARGET T0401 # 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 T0401.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 # # ============================================ # Comments from T0401.t2k.pb.rdb # ============================================ # TARGET T0401 # 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 T0401.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 # # ============================================ # Comments from T0401.t2k.bys.rdb # ============================================ # TARGET T0401 # 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 T0401.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 # # ============================================ # Comments from T0401.t2k.alpha.rdb # ============================================ # TARGET T0401 # 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 T0401.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 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.4930 0.1272 0.3799 2 E 0.5225 0.1540 0.3235 3 V 0.5182 0.2070 0.2748 4 I 0.4045 0.2697 0.3258 5 E 0.2856 0.3625 0.3519 6 S 0.1717 0.4594 0.3689 7 K 0.1157 0.5134 0.3709 8 W 0.1312 0.4943 0.3744 9 Y 0.1818 0.3879 0.4303 10 K 0.1716 0.3342 0.4942 11 K 0.1602 0.2622 0.5776 12 D 0.1266 0.1583 0.7151 13 G 0.0772 0.2194 0.7034 14 A 0.1352 0.2100 0.6548 15 S 0.1562 0.1341 0.7098 16 S 0.0229 0.6757 0.3014 17 A 0.0132 0.8163 0.1705 18 S 0.0220 0.8227 0.1553 19 I 0.0122 0.8759 0.1118 20 D 0.0107 0.9007 0.0885 21 D 0.0102 0.9149 0.0750 22 V 0.0098 0.9149 0.0753 23 E 0.0092 0.9159 0.0749 24 K 0.0089 0.9032 0.0879 25 L 0.0180 0.7863 0.1957 26 L 0.0551 0.4422 0.5027 27 N 0.0561 0.1296 0.8142 28 T 0.2036 0.0655 0.7310 29 T 0.3134 0.0743 0.6123 30 L 0.2719 0.0382 0.6899 31 P 0.1457 0.2743 0.5801 32 K 0.0276 0.6383 0.3341 33 Q 0.0331 0.7311 0.2358 34 Y 0.0404 0.7766 0.1829 35 K 0.0252 0.8618 0.1130 36 S 0.0450 0.8547 0.1003 37 F 0.0688 0.8279 0.1034 38 L 0.1085 0.7720 0.1195 39 L 0.1412 0.6935 0.1653 40 W 0.1559 0.5232 0.3209 41 S 0.1553 0.3290 0.5156 42 N 0.1134 0.1552 0.7314 43 G 0.1117 0.1053 0.7830 44 G 0.2719 0.0902 0.6379 45 E 0.4826 0.0853 0.4321 46 G 0.4759 0.0762 0.4479 47 K 0.4480 0.0813 0.4706 48 L 0.2834 0.1074 0.6092 49 G 0.1632 0.0881 0.7487 50 D 0.1829 0.1255 0.6917 51 N 0.2676 0.0981 0.6343 52 Y 0.5559 0.0416 0.4025 53 I 0.6922 0.0178 0.2900 54 Y 0.7600 0.0155 0.2245 55 I 0.7164 0.0357 0.2479 56 W 0.5710 0.0763 0.3527 57 A 0.3289 0.1219 0.5491 58 I 0.1211 0.5066 0.3722 59 E 0.0485 0.7276 0.2239 60 D 0.0453 0.7890 0.1656 61 V 0.0395 0.8363 0.1241 62 I 0.0380 0.8445 0.1175 63 A 0.0594 0.7819 0.1587 64 Y 0.0975 0.6188 0.2836 65 N 0.1185 0.3827 0.4988 66 H 0.0362 0.6408 0.3230 67 D 0.0419 0.5860 0.3722 68 Y 0.0811 0.5031 0.4158 69 G 0.1137 0.4943 0.3920 70 I 0.1178 0.6185 0.2636 71 Q 0.0908 0.6796 0.2296 72 K 0.1363 0.6762 0.1875 73 Y 0.1396 0.5327 0.3277 74 L 0.1895 0.3111 0.4994 75 Q 0.1245 0.2386 0.6368 76 K 0.0932 0.1506 0.7562 77 E 0.3608 0.0506 0.5887 78 Y 0.6864 0.0187 0.2948 79 W 0.7688 0.0109 0.2203 80 A 0.7390 0.0172 0.2438 81 F 0.5592 0.0308 0.4100 82 G 0.3206 0.0697 0.6097 83 M 0.1910 0.1515 0.6575 84 D 0.1426 0.1518 0.7056 85 G 0.1717 0.1105 0.7178 86 D 0.3576 0.0771 0.5653 87 I 0.6356 0.0327 0.3317 88 G 0.7584 0.0128 0.2287 89 Y 0.8117 0.0067 0.1816 90 I 0.8127 0.0061 0.1811 91 L 0.7950 0.0096 0.1954 92 H 0.7104 0.0134 0.2763 93 L 0.4689 0.0667 0.4644 94 S 0.2308 0.1202 0.6489 95 D 0.1423 0.1253 0.7324 96 N 0.1746 0.1132 0.7122 97 S 0.3417 0.0455 0.6129 98 I 0.5737 0.0210 0.4053 99 Y 0.6971 0.0149 0.2880 100 R 0.7523 0.0080 0.2397 101 V 0.7017 0.0144 0.2838 102 D 0.5068 0.0252 0.4681 103 L 0.2529 0.1773 0.5698 104 G 0.1550 0.1541 0.6909 105 D 0.2020 0.1179 0.6801 106 L 0.2446 0.1128 0.6426 107 D 0.1948 0.0538 0.7514 108 I 0.0498 0.5806 0.3696 109 T 0.0537 0.5912 0.3551 110 S 0.1285 0.5149 0.3566 111 I 0.2248 0.4723 0.3029 112 K 0.2999 0.4087 0.2914 113 Y 0.3289 0.3720 0.2991 114 I 0.3175 0.2933 0.3892 115 A 0.2009 0.2139 0.5852 116 P 0.0671 0.5234 0.4095 117 S 0.0877 0.4283 0.4840 118 F 0.0334 0.6983 0.2683 119 D 0.0138 0.8414 0.1448 120 D 0.0112 0.8966 0.0922 121 F 0.0142 0.8829 0.1029 122 L 0.0281 0.8206 0.1513 123 G 0.0283 0.7444 0.2273 124 K 0.0412 0.6247 0.3340 125 A 0.1044 0.4790 0.4166 126 I 0.1926 0.3987 0.4087 127 Y 0.2480 0.3210 0.4310 128 L 0.2429 0.3236 0.4335 129 N 0.2004 0.2792 0.5204 130 F 0.1018 0.5113 0.3869 131 N 0.0786 0.5932 0.3281 132 K 0.0906 0.6010 0.3083 133 L 0.0836 0.6510 0.2654 134 Q 0.0931 0.6228 0.2841 135 N 0.1091 0.5315 0.3594 136 V 0.1304 0.4724 0.3972 137 A 0.1422 0.3584 0.4994 138 N 0.1553 0.2520 0.5927 139 N 0.1394 0.2782 0.5824 140 N 0.1760 0.1803 0.6437 141 L 0.1804 0.2378 0.5818 142 T 0.2142 0.1702 0.6155 143 T 0.1837 0.1232 0.6930