# This file is the result of combining several RDB files, specifically # T0474.t04.str2.rdb (weight 1.54425) # T0474.t04.str4.rdb (weight 0.924988) # T0474.t04.pb.rdb (weight 0.789901) # T0474.t04.bys.rdb (weight 0.748322) # T0474.t04.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 T0474.t04.str2.rdb # ============================================ # TARGET T0474 # 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 T0474.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 16.4906 # # ============================================ # Comments from T0474.t04.str4.rdb # ============================================ # TARGET T0474 # 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 T0474.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 16.4906 # # ============================================ # Comments from T0474.t04.pb.rdb # ============================================ # TARGET T0474 # 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 T0474.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 16.4906 # # ============================================ # Comments from T0474.t04.bys.rdb # ============================================ # TARGET T0474 # 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 T0474.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 16.4906 # # ============================================ # Comments from T0474.t04.alpha.rdb # ============================================ # TARGET T0474 # 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 T0474.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 16.4906 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.2320 0.2324 0.5356 2 N 0.1992 0.2717 0.5290 3 S 0.1472 0.4940 0.3588 4 L 0.1201 0.5600 0.3200 5 A 0.1099 0.5677 0.3224 6 G 0.1026 0.5806 0.3168 7 I 0.1037 0.6691 0.2272 8 D 0.1336 0.5806 0.2858 9 M 0.2039 0.4407 0.3555 10 G 0.2525 0.3771 0.3703 11 R 0.4119 0.2821 0.3060 12 I 0.6120 0.1349 0.2531 13 L 0.6592 0.0785 0.2623 14 L 0.6745 0.0547 0.2708 15 D 0.3901 0.0535 0.5564 16 L 0.2146 0.1364 0.6490 17 S 0.1206 0.1924 0.6870 18 N 0.0129 0.7069 0.2802 19 E 0.0109 0.8465 0.1426 20 V 0.0093 0.9073 0.0834 21 I 0.0084 0.9136 0.0780 22 K 0.0089 0.9008 0.0904 23 Q 0.0100 0.8957 0.0943 24 L 0.0100 0.8994 0.0906 25 D 0.0096 0.8903 0.1001 26 D 0.0101 0.8956 0.0944 27 L 0.0103 0.8947 0.0950 28 E 0.0114 0.8928 0.0958 29 V 0.0148 0.8650 0.1202 30 Q 0.0324 0.7252 0.2424 31 R 0.0620 0.3444 0.5937 32 N 0.0560 0.1510 0.7930 33 L 0.1710 0.0559 0.7731 34 P 0.1457 0.0754 0.7788 35 R 0.0295 0.6895 0.2810 36 A 0.0100 0.8409 0.1491 37 D 0.0086 0.9112 0.0802 38 L 0.0084 0.9172 0.0745 39 L 0.0086 0.9090 0.0824 40 R 0.0083 0.9201 0.0716 41 E 0.0083 0.9221 0.0696 42 A 0.0083 0.9225 0.0692 43 V 0.0084 0.9170 0.0747 44 D 0.0083 0.9198 0.0719 45 Q 0.0084 0.9170 0.0745 46 Y 0.0086 0.9124 0.0790 47 L 0.0092 0.9008 0.0900 48 I 0.0122 0.8581 0.1298 49 N 0.0318 0.6390 0.3292 50 Q 0.0740 0.3520 0.5739 51 S 0.1047 0.2571 0.6382 52 Q 0.1057 0.3594 0.5349 53 T 0.1174 0.4068 0.4758 54 A 0.0956 0.5641 0.3404 55 R 0.0881 0.5410 0.3708 56 T 0.0919 0.5037 0.4044 57 S 0.1533 0.2820 0.5647 58 V 0.2247 0.1788 0.5965 59 P 0.1978 0.2436 0.5586 60 G 0.2587 0.2444 0.4970 61 I 0.3246 0.2728 0.4026 62 W 0.4044 0.1979 0.3977 63 Q 0.3129 0.1785 0.5086 64 G 0.1620 0.1422 0.6957 65 C 0.1883 0.1342 0.6775 66 E 0.1798 0.1793 0.6409 67 E 0.1491 0.3176 0.5332 68 D 0.1572 0.2940 0.5488 69 G 0.1823 0.3973 0.4203 70 V 0.0830 0.7081 0.2089 71 E 0.0405 0.8324 0.1272 72 Y 0.0245 0.8665 0.1090 73 Q 0.0123 0.8990 0.0887 74 R 0.0104 0.9052 0.0844 75 K 0.0116 0.8970 0.0914 76 L 0.0203 0.8548 0.1249 77 R 0.0260 0.8402 0.1338 78 E 0.0180 0.8376 0.1444 79 E 0.0373 0.7338 0.2289 80 W 0.0770 0.5271 0.3959