# 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) # T0393.t04.str2.rdb (weight 1.54425) # T0393.t04.str4.rdb (weight 0.924988) # T0393.t04.pb.rdb (weight 0.789901) # T0393.t04.bys.rdb (weight 0.748322) # T0393.t04.alpha.rdb (weight 0.678173) # T0393.t2k.str2.rdb (weight 1.54425) # T0393.t2k.str4.rdb (weight 0.924988) # T0393.t2k.pb.rdb (weight 0.789901) # T0393.t2k.bys.rdb (weight 0.748322) # T0393.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 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 # # ============================================ # Comments from T0393.t04.str2.rdb # ============================================ # TARGET T0393 # Using neural net dunbrack-40pc-3157-t04-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.t04-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 24.6639 # # ============================================ # Comments from T0393.t04.str4.rdb # ============================================ # TARGET T0393 # Using neural net dunbrack-40pc-3157-t04-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.t04-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 24.6639 # # ============================================ # Comments from T0393.t04.pb.rdb # ============================================ # TARGET T0393 # Using neural net dunbrack-40pc-3157-t04-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.t04-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 24.6639 # # ============================================ # Comments from T0393.t04.bys.rdb # ============================================ # TARGET T0393 # Using neural net dunbrack-40pc-3157-t04-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.t04-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 24.6639 # # ============================================ # Comments from T0393.t04.alpha.rdb # ============================================ # TARGET T0393 # Using neural net dunbrack-40pc-3157-t04-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.t04-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 24.6639 # # ============================================ # Comments from T0393.t2k.str2.rdb # ============================================ # TARGET T0393 # 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 T0393.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 24.1977 # # ============================================ # Comments from T0393.t2k.str4.rdb # ============================================ # TARGET T0393 # 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 T0393.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 24.1977 # # ============================================ # Comments from T0393.t2k.pb.rdb # ============================================ # TARGET T0393 # 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 T0393.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 24.1977 # # ============================================ # Comments from T0393.t2k.bys.rdb # ============================================ # TARGET T0393 # 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 T0393.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 24.1977 # # ============================================ # Comments from T0393.t2k.alpha.rdb # ============================================ # TARGET T0393 # 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 T0393.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 24.1977 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 Y 0.5415 0.0332 0.4252 2 D 0.4604 0.0291 0.5105 3 A 0.4169 0.0471 0.5361 4 D 0.2029 0.0301 0.7670 5 S 0.0412 0.5462 0.4127 6 E 0.0310 0.5763 0.3927 7 Q 0.0797 0.5547 0.3656 8 R 0.0793 0.6275 0.2932 9 K 0.0625 0.7254 0.2121 10 S 0.0662 0.7640 0.1697 11 L 0.0731 0.7690 0.1580 12 H 0.0720 0.7861 0.1419 13 L 0.0658 0.8157 0.1186 14 A 0.0722 0.8083 0.1196 15 A 0.0788 0.8153 0.1059 16 V 0.0901 0.7996 0.1103 17 F 0.0856 0.7797 0.1347 18 T 0.0641 0.7713 0.1647 19 C 0.0353 0.7787 0.1860 20 N 0.0321 0.7736 0.1944 21 F 0.0180 0.8181 0.1639 22 T 0.0112 0.8947 0.0941 23 N 0.0092 0.9155 0.0753 24 H 0.0085 0.9206 0.0710 25 M 0.0083 0.9227 0.0690 26 Y 0.0083 0.9230 0.0687 27 A 0.0083 0.9225 0.0692 28 L 0.0083 0.9232 0.0685 29 A 0.0083 0.9207 0.0710 30 A 0.0083 0.9221 0.0696 31 E 0.0083 0.9245 0.0672 32 L 0.0083 0.9222 0.0694 33 L 0.0084 0.9171 0.0745 34 K 0.0087 0.8950 0.0963 35 K 0.0138 0.7998 0.1864 36 Y 0.0573 0.3071 0.6356 37 N 0.0455 0.0724 0.8821 38 L 0.1598 0.0269 0.8133 39 P 0.1886 0.0876 0.7237 40 F 0.1226 0.4902 0.3872 41 D 0.0981 0.6320 0.2699 42 V 0.1770 0.6009 0.2221 43 M 0.1547 0.6391 0.2061 44 L 0.0643 0.7570 0.1787 45 P 0.0176 0.8556 0.1268 46 L 0.0174 0.8373 0.1453 47 I 0.0130 0.8680 0.1190 48 D 0.0096 0.8702 0.1202 49 E 0.0096 0.8795 0.1110 50 T 0.0136 0.8663 0.1201 51 A 0.0099 0.8676 0.1225 52 R 0.0088 0.8982 0.0930 53 K 0.0102 0.8718 0.1180 54 V 0.0181 0.8413 0.1406 55 H 0.0269 0.7898 0.1833 56 E 0.0438 0.6162 0.3400 57 L 0.1056 0.3469 0.5475 58 E 0.1644 0.1098 0.7258 59 P 0.0888 0.4303 0.4809 60 K 0.0628 0.5733 0.3638 61 T 0.1019 0.5590 0.3392 62 A 0.1509 0.4529 0.3962 63 Q 0.1907 0.3123 0.4970 64 T 0.2001 0.2247 0.5752 65 G 0.2019 0.1932 0.6049 66 P 0.2065 0.3009 0.4926 67 A 0.2059 0.4251 0.3690 68 I 0.2164 0.4339 0.3497 69 R 0.1909 0.3883 0.4208 70 Y 0.1238 0.3483 0.5279 71 D 0.1411 0.2705 0.5884 72 E 0.0148 0.7694 0.2158 73 N 0.0135 0.8482 0.1383 74 V 0.0175 0.8851 0.0974 75 I 0.0105 0.9056 0.0839 76 G 0.0093 0.9087 0.0820 77 N 0.0094 0.9025 0.0881 78 H 0.0130 0.8900 0.0971 79 L 0.0098 0.8979 0.0923 80 R 0.0092 0.8921 0.0987 81 M 0.0134 0.7883 0.1983 82 L 0.0334 0.6472 0.3194 83 A 0.0354 0.5405 0.4242 84 D 0.0526 0.3483 0.5990 85 D 0.1017 0.2992 0.5991 86 P 0.0154 0.7439 0.2408 87 A 0.0121 0.8421 0.1458 88 M 0.0098 0.9098 0.0803 89 Q 0.0086 0.9184 0.0730 90 R 0.0084 0.9195 0.0721 91 L 0.0090 0.9167 0.0742 92 Y 0.0088 0.9142 0.0770 93 E 0.0091 0.9061 0.0848 94 L 0.0128 0.8756 0.1116 95 L 0.0259 0.8053 0.1689 96 S 0.0322 0.7648 0.2030 97 R 0.0341 0.7392 0.2267 98 S 0.0778 0.6291 0.2931 99 I 0.0944 0.6292 0.2764 100 H 0.1021 0.5607 0.3372 101 E 0.1114 0.4831 0.4055 102 R 0.1426 0.3196 0.5379 103 Q 0.1574 0.2085 0.6341