# This file is the result of combining several RDB files, specifically # T0574.t06.str2.rdb (weight 1.54425) # T0574.t06.str4.rdb (weight 0.924988) # T0574.t06.pb.rdb (weight 0.789901) # T0574.t06.bys.rdb (weight 0.748322) # T0574.t06.alpha.rdb (weight 0.678173) # T0574.t04.str2.rdb (weight 1.54425) # T0574.t04.str4.rdb (weight 0.924988) # T0574.t04.pb.rdb (weight 0.789901) # T0574.t04.bys.rdb (weight 0.748322) # T0574.t04.alpha.rdb (weight 0.678173) # T0574.t2k.str2.rdb (weight 1.54425) # T0574.t2k.str4.rdb (weight 0.924988) # T0574.t2k.pb.rdb (weight 0.789901) # T0574.t2k.bys.rdb (weight 0.748322) # T0574.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 T0574.t06.str2.rdb # ============================================ # TARGET T0574 # 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 T0574.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 8.57718 # # ============================================ # Comments from T0574.t06.str4.rdb # ============================================ # TARGET T0574 # 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 T0574.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 8.57718 # # ============================================ # Comments from T0574.t06.pb.rdb # ============================================ # TARGET T0574 # 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 T0574.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 8.57718 # # ============================================ # Comments from T0574.t06.bys.rdb # ============================================ # TARGET T0574 # 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 T0574.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 8.57718 # # ============================================ # Comments from T0574.t06.alpha.rdb # ============================================ # TARGET T0574 # 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 T0574.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 8.57718 # # ============================================ # Comments from T0574.t04.str2.rdb # ============================================ # TARGET T0574 # 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 T0574.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 8.70131 # # ============================================ # Comments from T0574.t04.str4.rdb # ============================================ # TARGET T0574 # 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 T0574.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 8.70131 # # ============================================ # Comments from T0574.t04.pb.rdb # ============================================ # TARGET T0574 # 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 T0574.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 8.70131 # # ============================================ # Comments from T0574.t04.bys.rdb # ============================================ # TARGET T0574 # 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 T0574.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 8.70131 # # ============================================ # Comments from T0574.t04.alpha.rdb # ============================================ # TARGET T0574 # 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 T0574.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 8.70131 # # ============================================ # Comments from T0574.t2k.str2.rdb # ============================================ # TARGET T0574 # 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 T0574.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 9.56554 # # ============================================ # Comments from T0574.t2k.str4.rdb # ============================================ # TARGET T0574 # 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 T0574.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 9.56554 # # ============================================ # Comments from T0574.t2k.pb.rdb # ============================================ # TARGET T0574 # 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 T0574.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 9.56554 # # ============================================ # Comments from T0574.t2k.bys.rdb # ============================================ # TARGET T0574 # 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 T0574.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 9.56554 # # ============================================ # Comments from T0574.t2k.alpha.rdb # ============================================ # TARGET T0574 # 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 T0574.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 9.56554 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.1121 0.5200 0.3679 2 K 0.0525 0.7034 0.2441 3 N 0.0259 0.8347 0.1394 4 A 0.0156 0.8845 0.0998 5 M 0.0101 0.9103 0.0797 6 A 0.0084 0.9205 0.0711 7 L 0.0083 0.9214 0.0702 8 T 0.0083 0.9226 0.0691 9 L 0.0083 0.9234 0.0683 10 A 0.0083 0.9222 0.0695 11 G 0.0085 0.9187 0.0728 12 L 0.0101 0.9048 0.0851 13 L 0.0155 0.8442 0.1404 14 A 0.0316 0.7498 0.2186 15 A 0.0663 0.6359 0.2978 16 P 0.0318 0.7707 0.1975 17 S 0.0388 0.7807 0.1805 18 L 0.0539 0.7603 0.1858 19 G 0.0631 0.7246 0.2123 20 F 0.0694 0.6501 0.2804 21 A 0.0953 0.5199 0.3848 22 A 0.1378 0.2847 0.5775 23 A 0.1996 0.0977 0.7026 24 P 0.1474 0.2409 0.6117 25 D 0.1592 0.1520 0.6887 26 A 0.3593 0.0912 0.5496 27 V 0.6824 0.0221 0.2955 28 M 0.7729 0.0082 0.2189 29 V 0.8057 0.0067 0.1876 30 F 0.7809 0.0084 0.2107 31 A 0.7222 0.0121 0.2657 32 R 0.5411 0.0232 0.4357 33 Q 0.3382 0.0770 0.5848 34 G 0.1924 0.1035 0.7042 35 D 0.2147 0.1253 0.6600 36 K 0.2511 0.1204 0.6286 37 G 0.3791 0.0822 0.5387 38 S 0.5795 0.0485 0.3720 39 V 0.6663 0.0399 0.2938 40 S 0.6095 0.0367 0.3538 41 V 0.4370 0.1225 0.4405 42 G 0.2477 0.1283 0.6241 43 D 0.2322 0.1520 0.6157 44 K 0.3389 0.1572 0.5039 45 H 0.4264 0.1379 0.4357 46 F 0.4669 0.1257 0.4074 47 R 0.5156 0.0914 0.3930 48 T 0.5252 0.0713 0.4036 49 Q 0.5689 0.0646 0.3665 50 A 0.6272 0.0405 0.3323 51 F 0.6892 0.0153 0.2955 52 K 0.7183 0.0093 0.2724 53 V 0.7972 0.0062 0.1966 54 R 0.7935 0.0069 0.1997 55 L 0.7715 0.0098 0.2187 56 V 0.6798 0.0401 0.2802 57 N 0.5145 0.0593 0.4261 58 A 0.2506 0.2025 0.5469 59 A 0.1960 0.2029 0.6011 60 K 0.1887 0.2255 0.5859 61 S 0.2947 0.1539 0.5514 62 E 0.4099 0.1215 0.4686 63 I 0.5446 0.0700 0.3854 64 S 0.3885 0.0787 0.5328 65 L 0.2336 0.2565 0.5098 66 K 0.1783 0.2114 0.6104 67 N 0.1890 0.1385 0.6725 68 S 0.3624 0.1158 0.5218 69 C 0.6252 0.0619 0.3129 70 L 0.7236 0.0377 0.2387 71 V 0.7647 0.0244 0.2109 72 A 0.7187 0.0317 0.2496 73 Q 0.6505 0.0390 0.3105 74 S 0.3859 0.0503 0.5638 75 A 0.1248 0.3323 0.5429 76 A 0.0769 0.1765 0.7466 77 G 0.0730 0.0935 0.8335 78 Q 0.3526 0.0304 0.6170 79 S 0.6214 0.0245 0.3542 80 F 0.6575 0.0233 0.3192 81 R 0.6255 0.0199 0.3546 82 L 0.4705 0.0759 0.4536 83 D 0.3696 0.0994 0.5310 84 T 0.3728 0.1612 0.4660 85 V 0.2632 0.2696 0.4671 86 D 0.2043 0.2665 0.5292 87 E 0.0534 0.6925 0.2541 88 E 0.0379 0.7084 0.2537 89 L 0.0637 0.6508 0.2854 90 T 0.0909 0.5343 0.3748 91 A 0.0747 0.5021 0.4232 92 D 0.0717 0.3769 0.5514 93 T 0.1877 0.2298 0.5825 94 L 0.3175 0.1109 0.5716 95 K 0.2606 0.0501 0.6893 96 P 0.1516 0.1118 0.7366 97 G 0.0683 0.0962 0.8355 98 A 0.3211 0.0461 0.6328 99 S 0.6008 0.0210 0.3782 100 V 0.6562 0.0255 0.3183 101 E 0.6115 0.0329 0.3556 102 G 0.6376 0.0211 0.3412 103 D 0.7672 0.0100 0.2228 104 A 0.7864 0.0073 0.2063 105 I 0.7998 0.0094 0.1908 106 F 0.7532 0.0104 0.2364 107 A 0.6170 0.0334 0.3496 108 S 0.3464 0.0380 0.6155 109 E 0.1575 0.2532 0.5893 110 D 0.1729 0.2414 0.5857 111 D 0.1099 0.5140 0.3761 112 A 0.1474 0.5211 0.3314 113 V 0.2294 0.4548 0.3158 114 Y 0.2761 0.2753 0.4486 115 G 0.3402 0.1495 0.5104 116 A 0.5067 0.1105 0.3827 117 S 0.6077 0.0762 0.3161 118 L 0.7320 0.0361 0.2319 119 V 0.7624 0.0213 0.2163 120 R 0.7297 0.0189 0.2515 121 L 0.6435 0.0458 0.3107 122 S 0.3749 0.0812 0.5439 123 D 0.1530 0.2838 0.5632 124 R 0.1292 0.2315 0.6393 125 C 0.1837 0.1463 0.6700 126 K 0.1554 0.1937 0.6509