# This file is the result of combining several RDB files, specifically # T0472.t2k.str2.rdb (weight 1.54425) # T0472.t2k.str4.rdb (weight 0.924988) # T0472.t2k.pb.rdb (weight 0.789901) # T0472.t2k.bys.rdb (weight 0.748322) # T0472.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 T0472.t2k.str2.rdb # ============================================ # TARGET T0472 # 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 T0472.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 17.4049 # # ============================================ # Comments from T0472.t2k.str4.rdb # ============================================ # TARGET T0472 # 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 T0472.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 17.4049 # # ============================================ # Comments from T0472.t2k.pb.rdb # ============================================ # TARGET T0472 # 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 T0472.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 17.4049 # # ============================================ # Comments from T0472.t2k.bys.rdb # ============================================ # TARGET T0472 # 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 T0472.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 17.4049 # # ============================================ # Comments from T0472.t2k.alpha.rdb # ============================================ # TARGET T0472 # 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 T0472.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 17.4049 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.3493 0.1212 0.5296 2 S 0.3410 0.0814 0.5777 3 G 0.4605 0.0727 0.4669 4 W 0.6976 0.0498 0.2525 5 Y 0.7596 0.0236 0.2168 6 E 0.7817 0.0144 0.2039 7 L 0.7569 0.0221 0.2210 8 S 0.6912 0.0404 0.2684 9 K 0.5718 0.0910 0.3372 10 S 0.3194 0.1042 0.5764 11 S 0.1826 0.1991 0.6182 12 N 0.1242 0.1526 0.7233 13 D 0.2014 0.0865 0.7122 14 Q 0.5422 0.0318 0.4260 15 F 0.7349 0.0104 0.2547 16 K 0.7969 0.0080 0.1951 17 F 0.8209 0.0050 0.1741 18 V 0.8226 0.0047 0.1727 19 L 0.7955 0.0057 0.1988 20 K 0.7400 0.0098 0.2502 21 A 0.4926 0.0305 0.4769 22 G 0.2668 0.0613 0.6718 23 N 0.1550 0.0826 0.7623 24 G 0.1671 0.0648 0.7681 25 E 0.5414 0.0165 0.4421 26 V 0.7316 0.0076 0.2608 27 I 0.7813 0.0101 0.2086 28 L 0.7653 0.0150 0.2197 29 T 0.6590 0.0328 0.3081 30 S 0.4681 0.0667 0.4652 31 E 0.2495 0.2955 0.4549 32 L 0.2112 0.3150 0.4738 33 Y 0.2622 0.2789 0.4588 34 T 0.1832 0.3368 0.4800 35 G 0.1340 0.3658 0.5002 36 K 0.0716 0.6302 0.2982 37 S 0.0466 0.6635 0.2899 38 G 0.0441 0.6619 0.2940 39 A 0.0362 0.7955 0.1682 40 M 0.0399 0.7568 0.2033 41 N 0.0374 0.6650 0.2977 42 G 0.0548 0.5774 0.3678 43 I 0.0722 0.7199 0.2080 44 E 0.0744 0.7707 0.1549 45 S 0.0962 0.7398 0.1639 46 V 0.0922 0.7276 0.1802 47 Q 0.1128 0.6316 0.2556 48 T 0.1017 0.4321 0.4661 49 N 0.0956 0.2045 0.6999 50 S 0.1395 0.1591 0.7015 51 P 0.0994 0.3615 0.5390 52 I 0.0692 0.5627 0.3681 53 E 0.0324 0.7775 0.1901 54 A 0.0370 0.7878 0.1752 55 R 0.0620 0.7510 0.1869 56 Y 0.1172 0.6888 0.1940 57 A 0.2193 0.5745 0.2061 58 K 0.3512 0.4200 0.2288 59 E 0.3828 0.3308 0.2863 60 V 0.3924 0.2668 0.3407 61 A 0.2442 0.2313 0.5246 62 K 0.1241 0.2815 0.5944 63 N 0.0793 0.1671 0.7536 64 D 0.0674 0.1025 0.8301 65 K 0.2646 0.0213 0.7140 66 P 0.5465 0.0291 0.4244 67 Y 0.7053 0.0225 0.2722 68 F 0.7876 0.0090 0.2034 69 N 0.7852 0.0077 0.2072 70 L 0.7802 0.0114 0.2085 71 K 0.6807 0.0408 0.2785 72 A 0.4552 0.0886 0.4562 73 A 0.2410 0.1324 0.6266 74 N 0.1323 0.0950 0.7727 75 H 0.1951 0.0988 0.7061 76 Q 0.4868 0.0352 0.4779 77 I 0.6600 0.0204 0.3196 78 I 0.6711 0.0315 0.2974 79 G 0.6039 0.0458 0.3503 80 T 0.4643 0.1090 0.4267 81 S 0.3526 0.1636 0.4838 82 Q 0.2104 0.3553 0.4343 83 M 0.2032 0.3953 0.4015 84 Y 0.2210 0.3748 0.4042 85 S 0.1766 0.4288 0.3946 86 S 0.1345 0.4864 0.3790 87 T 0.0297 0.7435 0.2268 88 A 0.0293 0.7834 0.1873 89 A 0.0283 0.7988 0.1729 90 R 0.0261 0.7978 0.1761 91 D 0.0355 0.6788 0.2857 92 N 0.0412 0.4426 0.5162 93 G 0.0588 0.3303 0.6109 94 I 0.0741 0.6449 0.2811 95 K 0.0764 0.7491 0.1746 96 S 0.0836 0.7750 0.1414 97 V 0.0732 0.7917 0.1351 98 M 0.0842 0.7227 0.1931 99 E 0.0627 0.5753 0.3621 100 N 0.0760 0.2845 0.6396 101 G 0.1239 0.1716 0.7046 102 K 0.1113 0.2371 0.6516 103 T 0.1396 0.1922 0.6682 104 T 0.2414 0.1753 0.5833 105 T 0.4065 0.1525 0.4410 106 I 0.4322 0.2025 0.3653 107 K 0.3997 0.2118 0.3885 108 D 0.3260 0.1678 0.5061 109 L 0.2177 0.2056 0.5767 110 T 0.1755 0.1325 0.6919