# This file is the result of combining several RDB files, specifically # T0393.t06.str2.rdb (weight 1.54425) # T0393.t06.str4.rdb (weight 0.924988) # T0393.t06.pb.rdb (weight 0.789901) # T0393.t06.bys.rdb (weight 0.748322) # T0393.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 T0393.t06.str2.rdb # ============================================ # TARGET T0393 # 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 T0393.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 25.1116 # # ============================================ # Comments from T0393.t06.str4.rdb # ============================================ # TARGET T0393 # 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 T0393.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 25.1116 # # ============================================ # Comments from T0393.t06.pb.rdb # ============================================ # TARGET T0393 # 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 T0393.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 25.1116 # # ============================================ # Comments from T0393.t06.bys.rdb # ============================================ # TARGET T0393 # 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 T0393.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 25.1116 # # ============================================ # Comments from T0393.t06.alpha.rdb # ============================================ # TARGET T0393 # 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 T0393.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 25.1116 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 Y 0.4395 0.0374 0.5231 2 D 0.3914 0.0314 0.5772 3 A 0.3410 0.0597 0.5993 4 D 0.1923 0.0593 0.7484 5 S 0.0235 0.6135 0.3630 6 E 0.0195 0.6694 0.3111 7 Q 0.0369 0.7188 0.2443 8 R 0.0482 0.7778 0.1740 9 K 0.0251 0.8523 0.1226 10 S 0.0285 0.8506 0.1209 11 L 0.0320 0.8637 0.1043 12 H 0.0239 0.8845 0.0916 13 L 0.0158 0.9028 0.0814 14 A 0.0134 0.9088 0.0778 15 A 0.0173 0.9047 0.0780 16 V 0.0199 0.8968 0.0833 17 F 0.0220 0.8860 0.0920 18 T 0.0293 0.8476 0.1232 19 C 0.0303 0.8156 0.1541 20 N 0.0258 0.7975 0.1767 21 F 0.0192 0.8561 0.1247 22 T 0.0119 0.9029 0.0852 23 N 0.0100 0.9132 0.0768 24 H 0.0091 0.9191 0.0718 25 M 0.0086 0.9215 0.0699 26 Y 0.0083 0.9218 0.0699 27 A 0.0083 0.9231 0.0686 28 L 0.0083 0.9226 0.0691 29 A 0.0083 0.9223 0.0694 30 A 0.0083 0.9209 0.0708 31 E 0.0083 0.9242 0.0675 32 L 0.0083 0.9233 0.0684 33 L 0.0084 0.9188 0.0728 34 K 0.0086 0.9068 0.0846 35 K 0.0127 0.8041 0.1832 36 Y 0.0583 0.3343 0.6074 37 N 0.0395 0.1061 0.8545 38 L 0.1647 0.0227 0.8126 39 P 0.1532 0.0837 0.7631 40 F 0.0594 0.5332 0.4073 41 D 0.0280 0.7318 0.2402 42 V 0.0373 0.7615 0.2013 43 M 0.0417 0.7811 0.1772 44 L 0.0223 0.8371 0.1406 45 P 0.0118 0.8848 0.1034 46 L 0.0134 0.8790 0.1076 47 I 0.0119 0.8912 0.0969 48 D 0.0094 0.9025 0.0881 49 E 0.0096 0.8906 0.0998 50 T 0.0136 0.8828 0.1036 51 A 0.0090 0.8990 0.0920 52 R 0.0089 0.8935 0.0976 53 K 0.0096 0.8768 0.1136 54 V 0.0183 0.8582 0.1235 55 H 0.0174 0.7674 0.2152 56 E 0.0348 0.5380 0.4272 57 L 0.1085 0.2723 0.6192 58 E 0.1466 0.1146 0.7387 59 P 0.0772 0.4503 0.4724 60 K 0.0580 0.5403 0.4018 61 T 0.0960 0.5314 0.3726 62 A 0.1769 0.3610 0.4621 63 Q 0.2121 0.2919 0.4961 64 T 0.2622 0.1883 0.5495 65 G 0.2624 0.1404 0.5972 66 P 0.2394 0.2373 0.5234 67 A 0.2387 0.3599 0.4014 68 I 0.2221 0.3795 0.3984 69 R 0.1632 0.3658 0.4710 70 Y 0.1185 0.3318 0.5497 71 D 0.1432 0.3618 0.4950 72 E 0.0162 0.7444 0.2393 73 N 0.0142 0.8402 0.1456 74 V 0.0207 0.8766 0.1026 75 I 0.0120 0.9056 0.0824 76 G 0.0088 0.9113 0.0799 77 N 0.0092 0.9070 0.0839 78 H 0.0110 0.9043 0.0847 79 L 0.0089 0.9104 0.0806 80 R 0.0089 0.9070 0.0841 81 M 0.0102 0.8633 0.1264 82 L 0.0209 0.7874 0.1916 83 A 0.0202 0.6739 0.3059 84 D 0.0412 0.4534 0.5054 85 D 0.1362 0.2055 0.6583 86 P 0.0128 0.7110 0.2762 87 A 0.0114 0.7773 0.2113 88 M 0.0101 0.8967 0.0933 89 Q 0.0085 0.9165 0.0751 90 R 0.0083 0.9221 0.0696 91 L 0.0083 0.9228 0.0690 92 Y 0.0083 0.9228 0.0689 93 E 0.0083 0.9236 0.0682 94 L 0.0084 0.9192 0.0724 95 L 0.0088 0.9101 0.0812 96 S 0.0091 0.9044 0.0866 97 R 0.0091 0.9045 0.0865 98 S 0.0105 0.8831 0.1064 99 I 0.0185 0.8172 0.1642 100 H 0.0363 0.6801 0.2836 101 E 0.0786 0.4391 0.4823 102 R 0.1377 0.2128 0.6495 103 Q 0.1368 0.1464 0.7168