# This file is the result of combining several RDB files, specifically # T0464.t2k.str2.rdb (weight 1.54425) # T0464.t2k.str4.rdb (weight 0.924988) # T0464.t2k.pb.rdb (weight 0.789901) # T0464.t2k.bys.rdb (weight 0.748322) # T0464.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 T0464.t2k.str2.rdb # ============================================ # TARGET T0464 # 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 T0464.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 7.41067 # # ============================================ # Comments from T0464.t2k.str4.rdb # ============================================ # TARGET T0464 # 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 T0464.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 7.41067 # # ============================================ # Comments from T0464.t2k.pb.rdb # ============================================ # TARGET T0464 # 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 T0464.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 7.41067 # # ============================================ # Comments from T0464.t2k.bys.rdb # ============================================ # TARGET T0464 # 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 T0464.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 7.41067 # # ============================================ # Comments from T0464.t2k.alpha.rdb # ============================================ # TARGET T0464 # 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 T0464.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 7.41067 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.2227 0.1729 0.6044 2 D 0.1891 0.1394 0.6715 3 R 0.0215 0.7509 0.2275 4 K 0.0166 0.8295 0.1539 5 L 0.0311 0.8356 0.1332 6 L 0.0352 0.8415 0.1233 7 H 0.0687 0.7873 0.1440 8 L 0.1397 0.6496 0.2107 9 L 0.3395 0.3213 0.3392 10 C 0.3752 0.1532 0.4716 11 S 0.2752 0.0467 0.6781 12 P 0.0750 0.3852 0.5397 13 D 0.0740 0.3261 0.5999 14 T 0.1281 0.1990 0.6729 15 R 0.1682 0.1711 0.6608 16 Q 0.2899 0.0795 0.6306 17 P 0.3015 0.1216 0.5769 18 L 0.3677 0.2056 0.4267 19 S 0.4173 0.2153 0.3674 20 L 0.3254 0.3113 0.3633 21 L 0.1976 0.3963 0.4061 22 E 0.1018 0.4784 0.4198 23 S 0.0474 0.6045 0.3482 24 K 0.0295 0.6565 0.3140 25 G 0.0316 0.7034 0.2650 26 L 0.0177 0.8649 0.1174 27 E 0.0105 0.9047 0.0848 28 A 0.0120 0.8960 0.0921 29 L 0.0151 0.8811 0.1038 30 N 0.0132 0.8751 0.1117 31 K 0.0105 0.8830 0.1066 32 A 0.0172 0.8330 0.1498 33 I 0.0313 0.7601 0.2086 34 A 0.0515 0.6058 0.3427 35 S 0.0741 0.2684 0.6575 36 G 0.0883 0.1423 0.7694 37 T 0.2787 0.1283 0.5930 38 V 0.4619 0.1481 0.3900 39 Q 0.5073 0.1418 0.3509 40 R 0.4104 0.1624 0.4272 41 A 0.2402 0.2506 0.5092 42 D 0.1304 0.1405 0.7291 43 G 0.0950 0.1216 0.7834 44 S 0.2569 0.0988 0.6443 45 I 0.3855 0.1838 0.4307 46 Q 0.3096 0.2444 0.4460 47 N 0.2640 0.2664 0.4697 48 Q 0.2311 0.2869 0.4820 49 S 0.1725 0.3951 0.4324 50 L 0.1219 0.4856 0.3925 51 H 0.0911 0.5647 0.3442 52 E 0.0731 0.6355 0.2915 53 A 0.1193 0.5583 0.3224 54 L 0.2491 0.3588 0.3921 55 I 0.3400 0.2075 0.4525 56 T 0.2460 0.1305 0.6236 57 R 0.0900 0.4060 0.5040 58 D 0.0979 0.3382 0.5640 59 R 0.1211 0.4393 0.4396 60 K 0.1643 0.4394 0.3962 61 Q 0.3108 0.3139 0.3753 62 V 0.4456 0.1759 0.3785 63 F 0.5798 0.0671 0.3531 64 R 0.5040 0.0662 0.4298 65 I 0.3220 0.1462 0.5318 66 E 0.2161 0.2154 0.5684 67 D 0.1384 0.1619 0.6997 68 S 0.1988 0.1156 0.6855 69 I 0.4264 0.0338 0.5398 70 P 0.5855 0.0336 0.3810 71 V 0.6910 0.0303 0.2787 72 L 0.6357 0.0331 0.3312 73 L 0.2686 0.0262 0.7052 74 P 0.1026 0.3576 0.5398 75 E 0.0315 0.6481 0.3205 76 E 0.0353 0.6868 0.2779 77 A 0.0608 0.6810 0.2582 78 I 0.0914 0.6603 0.2483 79 A 0.0737 0.7009 0.2254 80 T 0.0714 0.7060 0.2226 81 I 0.1067 0.6797 0.2136 82 Q 0.1624 0.5863 0.2513 83 I 0.2198 0.4865 0.2937 84 A 0.2408 0.3318 0.4275 85 N 0.1981 0.1789 0.6230 86 F 0.2051 0.0693 0.7256 87 P 0.1403 0.1774 0.6823 88 D 0.1034 0.2463 0.6503 89 K 0.1321 0.2236 0.6443