# This file is the result of combining several RDB files, specifically # TR464.t06.str2.rdb (weight 1.54425) # TR464.t06.str4.rdb (weight 0.924988) # TR464.t06.pb.rdb (weight 0.789901) # TR464.t06.bys.rdb (weight 0.748322) # TR464.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 TR464.t06.str2.rdb # ============================================ # TARGET TR464 # 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 TR464.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 3.69861 # # ============================================ # Comments from TR464.t06.str4.rdb # ============================================ # TARGET TR464 # 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 TR464.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 3.69861 # # ============================================ # Comments from TR464.t06.pb.rdb # ============================================ # TARGET TR464 # 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 TR464.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 3.69861 # # ============================================ # Comments from TR464.t06.bys.rdb # ============================================ # TARGET TR464 # 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 TR464.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 3.69861 # # ============================================ # Comments from TR464.t06.alpha.rdb # ============================================ # TARGET TR464 # 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 TR464.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 3.69861 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 L 0.2910 0.0866 0.6224 2 S 0.2628 0.1011 0.6362 3 L 0.1811 0.4124 0.4065 4 L 0.1466 0.4811 0.3723 5 E 0.1226 0.4800 0.3973 6 S 0.0894 0.5459 0.3646 7 K 0.0437 0.5856 0.3707 8 G 0.0430 0.6273 0.3297 9 L 0.0157 0.8357 0.1486 10 E 0.0089 0.9004 0.0907 11 A 0.0087 0.9070 0.0843 12 L 0.0109 0.8909 0.0981 13 N 0.0106 0.8903 0.0990 14 K 0.0089 0.8941 0.0970 15 A 0.0111 0.8675 0.1214 16 I 0.0252 0.8114 0.1634 17 A 0.0314 0.6673 0.3014 18 S 0.0633 0.3082 0.6284 19 G 0.0830 0.1136 0.8034 20 T 0.2710 0.1103 0.6187 21 V 0.4902 0.1059 0.4039 22 Q 0.4557 0.1687 0.3755 23 R 0.4622 0.1636 0.3742 24 A 0.3364 0.1902 0.4734 25 D 0.1835 0.1080 0.7086 26 G 0.0968 0.1094 0.7938 27 S 0.2118 0.1220 0.6662 28 I 0.2737 0.2268 0.4994 29 Q 0.2283 0.2645 0.5071 30 N 0.2400 0.1914 0.5686 31 Q 0.2856 0.1042 0.6102 32 S 0.2237 0.1215 0.6548 33 L 0.1219 0.4378 0.4403 34 H 0.1194 0.4891 0.3915 35 E 0.2507 0.4316 0.3177 36 A 0.4291 0.2463 0.3246 37 L 0.5819 0.1421 0.2761 38 I 0.6059 0.0789 0.3152 39 T 0.4535 0.0699 0.4766 40 R 0.2065 0.2005 0.5930 41 D 0.1849 0.1386 0.6765 42 R 0.1230 0.3199 0.5571 43 K 0.2247 0.2755 0.4998 44 Q 0.4744 0.1302 0.3955 45 V 0.6147 0.0425 0.3428 46 F 0.6895 0.0310 0.2795 47 R 0.7024 0.0219 0.2757 48 I 0.6008 0.0705 0.3288 49 E 0.4023 0.1430 0.4547 50 D 0.2421 0.1454 0.6125 51 S 0.2072 0.1217 0.6710 52 I 0.3462 0.0571 0.5967 53 P 0.4396 0.0726 0.4878 54 V 0.5830 0.0885 0.3285 55 L 0.5049 0.1051 0.3900 56 L 0.3761 0.1518 0.4721 57 P 0.1422 0.4779 0.3799 58 E 0.0425 0.6959 0.2617 59 E 0.0359 0.7173 0.2467 60 A 0.0526 0.7032 0.2442 61 I 0.1075 0.6499 0.2426 62 A 0.0740 0.7016 0.2245 63 T 0.0500 0.7793 0.1706 64 I 0.0553 0.7767 0.1680 65 Q 0.0772 0.7282 0.1946 66 I 0.1344 0.5972 0.2684 67 A 0.1299 0.4651 0.4050 68 N 0.1226 0.3075 0.5699 69 F 0.1413 0.2077 0.6510