# This file is the result of combining several RDB files, specifically # TR488.t06.str2.rdb (weight 1.54425) # TR488.t06.str4.rdb (weight 0.924988) # TR488.t06.pb.rdb (weight 0.789901) # TR488.t06.bys.rdb (weight 0.748322) # TR488.t06.alpha.rdb (weight 0.678173) # TR488.t04.str2.rdb (weight 1.54425) # TR488.t04.str4.rdb (weight 0.924988) # TR488.t04.pb.rdb (weight 0.789901) # TR488.t04.bys.rdb (weight 0.748322) # TR488.t04.alpha.rdb (weight 0.678173) # TR488.t2k.str2.rdb (weight 1.54425) # TR488.t2k.str4.rdb (weight 0.924988) # TR488.t2k.pb.rdb (weight 0.789901) # TR488.t2k.bys.rdb (weight 0.748322) # TR488.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 TR488.t06.str2.rdb # ============================================ # TARGET TR488 # 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 TR488.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 2908 # # ============================================ # Comments from TR488.t06.str4.rdb # ============================================ # TARGET TR488 # 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 TR488.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 2908 # # ============================================ # Comments from TR488.t06.pb.rdb # ============================================ # TARGET TR488 # 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 TR488.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 2908 # # ============================================ # Comments from TR488.t06.bys.rdb # ============================================ # TARGET TR488 # 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 TR488.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 2908 # # ============================================ # Comments from TR488.t06.alpha.rdb # ============================================ # TARGET TR488 # 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 TR488.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 2908 # # ============================================ # Comments from TR488.t04.str2.rdb # ============================================ # TARGET TR488 # 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 TR488.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 1830 # # ============================================ # Comments from TR488.t04.str4.rdb # ============================================ # TARGET TR488 # 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 TR488.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 1830 # # ============================================ # Comments from TR488.t04.pb.rdb # ============================================ # TARGET TR488 # 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 TR488.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 1830 # # ============================================ # Comments from TR488.t04.bys.rdb # ============================================ # TARGET TR488 # 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 TR488.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 1830 # # ============================================ # Comments from TR488.t04.alpha.rdb # ============================================ # TARGET TR488 # 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 TR488.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 1830 # # ============================================ # Comments from TR488.t2k.str2.rdb # ============================================ # TARGET TR488 # 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 TR488.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 270.538 # # ============================================ # Comments from TR488.t2k.str4.rdb # ============================================ # TARGET TR488 # 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 TR488.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 270.538 # # ============================================ # Comments from TR488.t2k.pb.rdb # ============================================ # TARGET TR488 # 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 TR488.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 270.538 # # ============================================ # Comments from TR488.t2k.bys.rdb # ============================================ # TARGET TR488 # 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 TR488.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 270.538 # # ============================================ # Comments from TR488.t2k.alpha.rdb # ============================================ # TARGET TR488 # 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 TR488.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 270.538 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 S 0.2840 0.0744 0.6416 2 M 0.3633 0.0547 0.5820 3 E 0.5805 0.0255 0.3940 4 I 0.7538 0.0109 0.2353 5 L 0.7903 0.0094 0.2004 6 Q 0.8063 0.0058 0.1879 7 V 0.8094 0.0065 0.1841 8 A 0.7808 0.0100 0.2092 9 L 0.7492 0.0190 0.2318 10 H 0.6437 0.0293 0.3270 11 K 0.4651 0.0501 0.4849 12 R 0.2555 0.1263 0.6182 13 D 0.1850 0.1559 0.6591 14 S 0.1723 0.1401 0.6876 15 G 0.2518 0.0865 0.6617 16 E 0.4386 0.0864 0.4750 17 Q 0.5843 0.0384 0.3773 18 L 0.7285 0.0158 0.2557 19 G 0.7741 0.0101 0.2158 20 I 0.7852 0.0084 0.2064 21 K 0.7630 0.0147 0.2223 22 L 0.7095 0.0192 0.2713 23 V 0.5987 0.0373 0.3640 24 R 0.4469 0.0828 0.4703 25 R 0.2965 0.0912 0.6122 26 T 0.1653 0.1621 0.6726 27 D 0.1105 0.1571 0.7324 28 E 0.2342 0.0651 0.7007 29 P 0.2655 0.0894 0.6451 30 G 0.4384 0.0438 0.5178 31 V 0.7055 0.0084 0.2861 32 F 0.7764 0.0076 0.2161 33 I 0.7455 0.0126 0.2419 34 L 0.6566 0.0457 0.2976 35 D 0.6674 0.0433 0.2893 36 L 0.5343 0.0747 0.3910 37 L 0.3378 0.0663 0.5959 38 E 0.1607 0.1841 0.6553 39 G 0.1014 0.1252 0.7734 40 G 0.1649 0.1420 0.6931 41 L 0.1628 0.4189 0.4183 42 A 0.1425 0.5192 0.3384 43 A 0.1356 0.5401 0.3243 44 Q 0.1662 0.3836 0.4503 45 D 0.1111 0.1789 0.7099 46 G 0.1052 0.0941 0.8007 47 R 0.3767 0.0457 0.5775 48 L 0.5138 0.0388 0.4475 49 S 0.3330 0.0316 0.6354 50 S 0.2051 0.1781 0.6168 51 N 0.1189 0.1076 0.7735 52 D 0.3173 0.0620 0.6207 53 R 0.6355 0.0279 0.3366 54 V 0.7472 0.0217 0.2311 55 L 0.7573 0.0145 0.2282 56 A 0.7617 0.0156 0.2226 57 I 0.6354 0.0444 0.3203 58 N 0.3542 0.0535 0.5923 59 G 0.1613 0.0652 0.7735 60 H 0.4214 0.0364 0.5422 61 D 0.5063 0.0354 0.4583 62 L 0.3367 0.1704 0.4929 63 K 0.2322 0.2384 0.5294 64 Y 0.1481 0.1584 0.6935 65 G 0.1357 0.0775 0.7869 66 T 0.1594 0.0323 0.8083 67 P 0.0129 0.7404 0.2467 68 E 0.0093 0.8665 0.1242 69 L 0.0084 0.9213 0.0703 70 A 0.0083 0.9207 0.0710 71 A 0.0083 0.9242 0.0675 72 Q 0.0083 0.9250 0.0667 73 I 0.0083 0.9234 0.0683 74 I 0.0084 0.9129 0.0787 75 Q 0.0091 0.8661 0.1248 76 A 0.0182 0.7030 0.2788 77 S 0.0629 0.2752 0.6619 78 G 0.0594 0.1096 0.8309 79 E 0.1686 0.0871 0.7443 80 R 0.4544 0.0304 0.5152 81 V 0.6847 0.0110 0.3042 82 N 0.7790 0.0064 0.2146 83 L 0.8092 0.0048 0.1860 84 T 0.8103 0.0058 0.1838 85 I 0.7842 0.0059 0.2099 86 A 0.6989 0.0122 0.2888 87 R 0.4374 0.0129 0.5497 88 P 0.2192 0.0827 0.6981 89 G 0.1256 0.0937 0.7806 90 K 0.2010 0.0292 0.7698 91 P 0.1855 0.1212 0.6933 92 E 0.2191 0.2522 0.5287 93 I 0.2376 0.2626 0.4998 94 E 0.2568 0.1829 0.5603 95 L 0.2402 0.1536 0.6063