# This file is the result of combining several RDB files, specifically # TR464.t2k.str2.rdb (weight 1.54425) # TR464.t2k.str4.rdb (weight 0.924988) # TR464.t2k.pb.rdb (weight 0.789901) # TR464.t2k.bys.rdb (weight 0.748322) # TR464.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 TR464.t2k.str2.rdb # ============================================ # TARGET TR464 # 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 TR464.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 4.61938 # # ============================================ # Comments from TR464.t2k.str4.rdb # ============================================ # TARGET TR464 # 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 TR464.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 4.61938 # # ============================================ # Comments from TR464.t2k.pb.rdb # ============================================ # TARGET TR464 # 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 TR464.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 4.61938 # # ============================================ # Comments from TR464.t2k.bys.rdb # ============================================ # TARGET TR464 # 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 TR464.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 4.61938 # # ============================================ # Comments from TR464.t2k.alpha.rdb # ============================================ # TARGET TR464 # 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 TR464.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 4.61938 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 L 0.3607 0.0998 0.5395 2 S 0.2996 0.0987 0.6017 3 L 0.2445 0.3480 0.4075 4 L 0.1868 0.3687 0.4444 5 E 0.1158 0.4112 0.4730 6 S 0.0725 0.4814 0.4460 7 K 0.0373 0.5674 0.3953 8 G 0.0348 0.6045 0.3606 9 L 0.0194 0.8321 0.1485 10 E 0.0108 0.8921 0.0970 11 A 0.0107 0.8963 0.0930 12 L 0.0135 0.8898 0.0967 13 N 0.0116 0.8896 0.0988 14 K 0.0094 0.8997 0.0908 15 A 0.0144 0.8702 0.1154 16 I 0.0263 0.8113 0.1624 17 A 0.0514 0.6694 0.2792 18 S 0.0672 0.3275 0.6053 19 G 0.0903 0.1673 0.7424 20 T 0.3064 0.1258 0.5678 21 V 0.4986 0.1249 0.3765 22 Q 0.5574 0.1057 0.3369 23 R 0.4638 0.1183 0.4178 24 A 0.2711 0.2129 0.5160 25 D 0.1308 0.1359 0.7332 26 G 0.0913 0.1226 0.7861 27 S 0.2712 0.0784 0.6504 28 I 0.4358 0.1420 0.4222 29 Q 0.3629 0.1983 0.4388 30 N 0.3518 0.1989 0.4493 31 Q 0.3818 0.1227 0.4954 32 S 0.3066 0.2190 0.4744 33 L 0.1924 0.3615 0.4460 34 H 0.1286 0.4790 0.3925 35 E 0.1404 0.4985 0.3611 36 A 0.2648 0.3583 0.3770 37 L 0.4632 0.1924 0.3444 38 I 0.5311 0.1204 0.3485 39 T 0.3975 0.0903 0.5122 40 R 0.2087 0.2395 0.5519 41 D 0.1755 0.1539 0.6706 42 R 0.1383 0.3217 0.5400 43 K 0.2292 0.2870 0.4837 44 Q 0.4649 0.1404 0.3946 45 V 0.6152 0.0575 0.3273 46 F 0.6871 0.0274 0.2855 47 R 0.6392 0.0284 0.3324 48 I 0.4515 0.0989 0.4497 49 E 0.2820 0.1827 0.5353 50 D 0.1518 0.1559 0.6922 51 S 0.1912 0.1170 0.6918 52 I 0.4116 0.0349 0.5535 53 P 0.5613 0.0373 0.4014 54 V 0.6835 0.0348 0.2817 55 L 0.6307 0.0366 0.3327 56 L 0.3246 0.0302 0.6452 57 P 0.1306 0.3355 0.5339 58 E 0.0441 0.6226 0.3333 59 E 0.0439 0.6488 0.3073 60 A 0.0774 0.5848 0.3378 61 I 0.1293 0.5099 0.3607 62 A 0.0983 0.5397 0.3620 63 T 0.1012 0.5708 0.3280 64 I 0.1642 0.5579 0.2779 65 Q 0.2438 0.4818 0.2744 66 I 0.3156 0.3810 0.3034 67 A 0.3093 0.2723 0.4183 68 N 0.2226 0.1890 0.5883 69 F 0.1827 0.1629 0.6543 70 L 0.3607 0.0998 0.5395 71 S 0.2996 0.0987 0.6017 72 L 0.2445 0.3480 0.4075 73 L 0.1868 0.3687 0.4444 74 E 0.1158 0.4112 0.4730 75 S 0.0725 0.4814 0.4460 76 K 0.0373 0.5674 0.3953 77 G 0.0348 0.6045 0.3606 78 L 0.0194 0.8321 0.1485 79 E 0.0108 0.8921 0.0970 80 A 0.0107 0.8963 0.0930 81 L 0.0135 0.8898 0.0967 82 N 0.0116 0.8896 0.0988 83 K 0.0094 0.8997 0.0908 84 A 0.0144 0.8702 0.1154 85 I 0.0263 0.8113 0.1624 86 A 0.0514 0.6694 0.2792 87 S 0.0672 0.3275 0.6053 88 G 0.0903 0.1673 0.7424 89 T 0.3064 0.1258 0.5678 90 V 0.4986 0.1249 0.3765 91 Q 0.5574 0.1057 0.3369 92 R 0.4638 0.1183 0.4178 93 A 0.2711 0.2129 0.5160 94 D 0.1308 0.1359 0.7332 95 G 0.0913 0.1226 0.7861 96 S 0.2712 0.0784 0.6504 97 I 0.4358 0.1420 0.4222 98 Q 0.3629 0.1983 0.4388 99 N 0.3518 0.1989 0.4493 100 Q 0.3818 0.1227 0.4954 101 S 0.3066 0.2190 0.4744 102 L 0.1924 0.3615 0.4460 103 H 0.1286 0.4790 0.3925 104 E 0.1404 0.4985 0.3611 105 A 0.2648 0.3583 0.3770 106 L 0.4632 0.1924 0.3444 107 I 0.5311 0.1204 0.3485 108 T 0.3975 0.0903 0.5122 109 R 0.2087 0.2395 0.5519 110 D 0.1755 0.1539 0.6706 111 R 0.1383 0.3217 0.5400 112 K 0.2292 0.2870 0.4837 113 Q 0.4649 0.1404 0.3946 114 V 0.6152 0.0575 0.3273 115 F 0.6871 0.0274 0.2855 116 R 0.6392 0.0284 0.3324 117 I 0.4515 0.0989 0.4497 118 E 0.2820 0.1827 0.5353 119 D 0.1518 0.1559 0.6922 120 S 0.1912 0.1170 0.6918 121 I 0.4116 0.0349 0.5535 122 P 0.5613 0.0373 0.4014 123 V 0.6835 0.0348 0.2817 124 L 0.6307 0.0366 0.3327 125 L 0.3246 0.0302 0.6452 126 P 0.1306 0.3355 0.5339 127 E 0.0441 0.6226 0.3333 128 E 0.0439 0.6488 0.3073 129 A 0.0774 0.5848 0.3378 130 I 0.1293 0.5099 0.3607 131 A 0.0983 0.5397 0.3620 132 T 0.1012 0.5708 0.3280 133 I 0.1642 0.5579 0.2779 134 Q 0.2438 0.4818 0.2744 135 I 0.3156 0.3810 0.3034 136 A 0.3093 0.2723 0.4183 137 N 0.2226 0.1890 0.5883 138 F 0.1827 0.1629 0.6543