# This file is the result of combining several RDB files, specifically # T0523.t06.str2.rdb (weight 1.54425) # T0523.t06.str4.rdb (weight 0.924988) # T0523.t06.pb.rdb (weight 0.789901) # T0523.t06.bys.rdb (weight 0.748322) # T0523.t06.alpha.rdb (weight 0.678173) # T0523.t04.str2.rdb (weight 1.54425) # T0523.t04.str4.rdb (weight 0.924988) # T0523.t04.pb.rdb (weight 0.789901) # T0523.t04.bys.rdb (weight 0.748322) # T0523.t04.alpha.rdb (weight 0.678173) # T0523.t2k.str2.rdb (weight 1.54425) # T0523.t2k.str4.rdb (weight 0.924988) # T0523.t2k.pb.rdb (weight 0.789901) # T0523.t2k.bys.rdb (weight 0.748322) # T0523.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 T0523.t06.str2.rdb # ============================================ # TARGET T0523 # 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 T0523.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 26209 # # ============================================ # Comments from T0523.t06.str4.rdb # ============================================ # TARGET T0523 # 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 T0523.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 26209 # # ============================================ # Comments from T0523.t06.pb.rdb # ============================================ # TARGET T0523 # 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 T0523.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 26209 # # ============================================ # Comments from T0523.t06.bys.rdb # ============================================ # TARGET T0523 # 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 T0523.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 26209 # # ============================================ # Comments from T0523.t06.alpha.rdb # ============================================ # TARGET T0523 # 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 T0523.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 26209 # # ============================================ # Comments from T0523.t04.str2.rdb # ============================================ # TARGET T0523 # 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 T0523.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 5880 # # ============================================ # Comments from T0523.t04.str4.rdb # ============================================ # TARGET T0523 # 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 T0523.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 5880 # # ============================================ # Comments from T0523.t04.pb.rdb # ============================================ # TARGET T0523 # 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 T0523.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 5880 # # ============================================ # Comments from T0523.t04.bys.rdb # ============================================ # TARGET T0523 # 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 T0523.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 5880 # # ============================================ # Comments from T0523.t04.alpha.rdb # ============================================ # TARGET T0523 # 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 T0523.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 5880 # # ============================================ # Comments from T0523.t2k.str2.rdb # ============================================ # TARGET T0523 # 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 T0523.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 772 # # ============================================ # Comments from T0523.t2k.str4.rdb # ============================================ # TARGET T0523 # 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 T0523.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 772 # # ============================================ # Comments from T0523.t2k.pb.rdb # ============================================ # TARGET T0523 # 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 T0523.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 772 # # ============================================ # Comments from T0523.t2k.bys.rdb # ============================================ # TARGET T0523 # 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 T0523.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 772 # # ============================================ # Comments from T0523.t2k.alpha.rdb # ============================================ # TARGET T0523 # 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 T0523.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 772 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 P 0.1403 0.1252 0.7344 2 A 0.0149 0.7652 0.2199 3 I 0.0099 0.8623 0.1278 4 D 0.0091 0.9126 0.0783 5 Y 0.0087 0.9153 0.0760 6 K 0.0083 0.9205 0.0711 7 T 0.0083 0.9205 0.0711 8 A 0.0088 0.9092 0.0820 9 F 0.0110 0.8699 0.1191 10 H 0.0209 0.7432 0.2360 11 L 0.0624 0.3833 0.5543 12 A 0.1993 0.1151 0.6856 13 P 0.1955 0.1596 0.6450 14 I 0.2991 0.1066 0.5944 15 G 0.6310 0.0303 0.3387 16 L 0.7690 0.0093 0.2218 17 V 0.8018 0.0064 0.1919 18 L 0.7726 0.0086 0.2188 19 S 0.5805 0.0272 0.3923 20 R 0.3130 0.0975 0.5895 21 D 0.1519 0.1256 0.7226 22 R 0.2071 0.0910 0.7019 23 V 0.4893 0.0494 0.4613 24 I 0.5706 0.0913 0.3381 25 E 0.4848 0.1942 0.3210 26 D 0.3567 0.2913 0.3520 27 C 0.1745 0.4041 0.4214 28 N 0.1323 0.4824 0.3853 29 D 0.0118 0.8031 0.1850 30 E 0.0093 0.8845 0.1062 31 L 0.0091 0.9154 0.0755 32 A 0.0084 0.9193 0.0723 33 A 0.0086 0.9091 0.0823 34 I 0.0128 0.8178 0.1694 35 F 0.0359 0.5523 0.4118 36 R 0.0457 0.2088 0.7456 37 C 0.1431 0.1184 0.7385 38 A 0.1645 0.0585 0.7771 39 R 0.0274 0.6786 0.2940 40 A 0.0169 0.7620 0.2211 41 D 0.0393 0.7254 0.2354 42 L 0.0938 0.5694 0.3368 43 I 0.1162 0.2800 0.6038 44 G 0.1025 0.1402 0.7572 45 R 0.2018 0.0842 0.7140 46 S 0.2314 0.0744 0.6942 47 F 0.1674 0.4261 0.4065 48 E 0.1671 0.5248 0.3081 49 V 0.2773 0.3793 0.3434 50 L 0.3928 0.1570 0.4502 51 Y 0.2923 0.0438 0.6639 52 P 0.2003 0.0666 0.7331 53 S 0.1623 0.0824 0.7553 54 S 0.0329 0.4859 0.4812 55 D 0.0327 0.6133 0.3540 56 E 0.0413 0.7065 0.2522 57 F 0.0314 0.8085 0.1601 58 E 0.0175 0.8569 0.1256 59 R 0.0228 0.8298 0.1475 60 I 0.0312 0.7891 0.1797 61 G 0.0232 0.8076 0.1692 62 E 0.0175 0.8424 0.1402 63 R 0.0236 0.7865 0.1899 64 I 0.0416 0.7434 0.2150 65 S 0.0397 0.7594 0.2009 66 P 0.0192 0.8566 0.1242 67 V 0.0223 0.8583 0.1195 68 M 0.0288 0.8413 0.1299 69 I 0.0479 0.7313 0.2208 70 A 0.0697 0.5052 0.4252 71 H 0.0835 0.1794 0.7371 72 G 0.1035 0.1004 0.7961 73 S 0.2323 0.0861 0.6816 74 Y 0.2977 0.0901 0.6122 75 A 0.2824 0.1554 0.5622 76 D 0.2810 0.2256 0.4934 77 D 0.4225 0.1750 0.4025 78 R 0.6622 0.0709 0.2669 79 I 0.7251 0.0422 0.2327 80 M 0.7380 0.0282 0.2338 81 K 0.7007 0.0297 0.2696 82 R 0.5975 0.0272 0.3753 83 A 0.2751 0.1574 0.5675 84 G 0.0865 0.1300 0.7835 85 G 0.1318 0.0668 0.8014 86 E 0.4129 0.0176 0.5694 87 L 0.6870 0.0115 0.3015 88 F 0.7438 0.0124 0.2438 89 W 0.7845 0.0058 0.2097 90 C 0.8046 0.0073 0.1881 91 H 0.7984 0.0064 0.1952 92 V 0.7758 0.0109 0.2132 93 T 0.6784 0.0276 0.2940 94 G 0.6329 0.0312 0.3359 95 R 0.5976 0.0300 0.3724 96 A 0.5425 0.0576 0.3999 97 L 0.4653 0.0801 0.4546 98 D 0.2529 0.0497 0.6974 99 R 0.0625 0.3649 0.5726 100 T 0.0668 0.2231 0.7102 101 A 0.1644 0.0930 0.7426 102 P 0.2726 0.0914 0.6360 103 L 0.4527 0.1004 0.4468 104 A 0.5312 0.0822 0.3866 105 A 0.6954 0.0426 0.2620 106 G 0.7392 0.0208 0.2400 107 V 0.7839 0.0168 0.1993 108 W 0.7831 0.0156 0.2013 109 T 0.7486 0.0227 0.2287 110 F 0.5990 0.0682 0.3328 111 E 0.3840 0.1556 0.4603 112 D 0.2566 0.1639 0.5795 113 L 0.1248 0.4370 0.4383 114 S 0.1003 0.5088 0.3909 115 A 0.0356 0.7245 0.2398 116 T 0.0353 0.7838 0.1809 117 R 0.0441 0.8072 0.1487 118 R 0.0572 0.7533 0.1895 119 V 0.0972 0.6545 0.2482 120 A 0.1360 0.4962 0.3678