# This file is the result of combining several RDB files, specifically # T0487.t06.str2.rdb (weight 1.54425) # T0487.t06.str4.rdb (weight 0.924988) # T0487.t06.pb.rdb (weight 0.789901) # T0487.t06.bys.rdb (weight 0.748322) # T0487.t06.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 T0487.t06.str2.rdb # ============================================ # TARGET T0487 # 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 T0487.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 1 # # ============================================ # Comments from T0487.t06.str4.rdb # ============================================ # TARGET T0487 # 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 T0487.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 1 # # ============================================ # Comments from T0487.t06.pb.rdb # ============================================ # TARGET T0487 # 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 T0487.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 1 # # ============================================ # Comments from T0487.t06.bys.rdb # ============================================ # TARGET T0487 # 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 T0487.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 1 # # ============================================ # Comments from T0487.t06.alpha.rdb # ============================================ # TARGET T0487 # 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 T0487.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 1 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 I 0.4273 0.2622 0.3105 2 L 0.4096 0.3106 0.2799 3 C 0.3493 0.3767 0.2740 4 E 0.2526 0.4691 0.2783 5 M 0.2148 0.4833 0.3019 6 S 0.1437 0.5447 0.3115 7 L 0.0327 0.8113 0.1560 8 E 0.0217 0.8567 0.1216 9 A 0.0242 0.8806 0.0953 10 W 0.0259 0.8649 0.1092 11 L 0.0379 0.8212 0.1409 12 A 0.0420 0.6726 0.2854 13 Q 0.0594 0.3103 0.6303 14 G 0.0491 0.1294 0.8215 15 H 0.1862 0.0447 0.7691 16 P 0.1918 0.0834 0.7248 17 L 0.2215 0.0690 0.7095 18 P 0.1461 0.2543 0.5996 19 K 0.0883 0.5461 0.3655 20 R 0.1110 0.6025 0.2865 21 V 0.1394 0.5877 0.2729 22 R 0.1211 0.6074 0.2716 23 N 0.1151 0.5547 0.3302 24 A 0.0845 0.6075 0.3080 25 Y 0.1072 0.5037 0.3891 26 D 0.1068 0.4604 0.4328 27 R 0.1029 0.4965 0.4006 28 R 0.1298 0.4486 0.4217 29 T 0.1755 0.4757 0.3488 30 W 0.1450 0.6172 0.2378 31 E 0.1701 0.6294 0.2005 32 L 0.2206 0.5715 0.2079 33 L 0.2404 0.5208 0.2387 34 R 0.2804 0.3821 0.3375 35 L 0.2370 0.2279 0.5351 36 G 0.1444 0.1064 0.7492 37 E 0.1493 0.2102 0.6405 38 E 0.1821 0.1647 0.6533 39 D 0.1973 0.0461 0.7566 40 P 0.0474 0.4892 0.4634 41 K 0.0499 0.4849 0.4652 42 E 0.1336 0.3278 0.5385 43 L 0.2645 0.0577 0.6778 44 P 0.2725 0.0586 0.6688 45 L 0.2490 0.0474 0.7036 46 P 0.1491 0.1925 0.6584 47 G 0.1041 0.1883 0.7076 48 G 0.1667 0.1668 0.6665 49 L 0.3133 0.1477 0.5389 50 S 0.3661 0.1918 0.4422 51 L 0.3663 0.3058 0.3279 52 L 0.3050 0.3680 0.3270 53 D 0.2447 0.4102 0.3451 54 Y 0.2011 0.4341 0.3647 55 H 0.1897 0.3941 0.4162 56 A 0.1512 0.4156 0.4333 57 S 0.1282 0.3489 0.5229 58 K 0.1055 0.2482 0.6463 59 G 0.1355 0.1831 0.6814 60 R 0.3264 0.1664 0.5073 61 L 0.4127 0.1478 0.4394 62 Q 0.3227 0.1369 0.5404 63 G 0.2472 0.1086 0.6442 64 R 0.3104 0.1207 0.5689 65 E 0.1955 0.1688 0.6357 66 G 0.1340 0.1072 0.7588 67 G 0.2396 0.0596 0.7008 68 R 0.5182 0.0451 0.4368 69 V 0.6926 0.0318 0.2756 70 A 0.7244 0.0314 0.2442 71 W 0.7429 0.0276 0.2295 72 V 0.6820 0.0360 0.2820 73 A 0.5770 0.0421 0.3809 74 D 0.2877 0.0208 0.6915 75 P 0.0819 0.3135 0.6046 76 K 0.0840 0.2643 0.6517 77 D 0.1831 0.1046 0.7123 78 P 0.0880 0.3222 0.5898 79 R 0.1144 0.2251 0.6604 80 K 0.2346 0.0637 0.7016 81 P 0.2496 0.0688 0.6816 82 I 0.2819 0.0576 0.6605 83 P 0.2250 0.2094 0.5656 84 H 0.2447 0.2602 0.4950 85 L 0.2962 0.2607 0.4430 86 T 0.2663 0.1688 0.5650 87 G 0.2681 0.1224 0.6095 88 L 0.4545 0.0749 0.4706 89 L 0.5082 0.0459 0.4459 90 V 0.3978 0.0265 0.5756 91 P 0.2557 0.0516 0.6927