# This file is the result of combining several RDB files, specifically # T0393.t04.str2.rdb (weight 1.54425) # T0393.t04.str4.rdb (weight 0.924988) # T0393.t04.pb.rdb (weight 0.789901) # T0393.t04.bys.rdb (weight 0.748322) # T0393.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 T0393.t04.str2.rdb # ============================================ # TARGET T0393 # 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 T0393.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 24.6639 # # ============================================ # Comments from T0393.t04.str4.rdb # ============================================ # TARGET T0393 # 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 T0393.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 24.6639 # # ============================================ # Comments from T0393.t04.pb.rdb # ============================================ # TARGET T0393 # 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 T0393.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 24.6639 # # ============================================ # Comments from T0393.t04.bys.rdb # ============================================ # TARGET T0393 # 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 T0393.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 24.6639 # # ============================================ # Comments from T0393.t04.alpha.rdb # ============================================ # TARGET T0393 # 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 T0393.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 24.6639 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 Y 0.4354 0.0262 0.5385 2 D 0.3998 0.0240 0.5761 3 A 0.3496 0.0921 0.5584 4 D 0.1902 0.1233 0.6865 5 S 0.0229 0.6323 0.3447 6 E 0.0194 0.7254 0.2552 7 Q 0.0331 0.7202 0.2467 8 R 0.0459 0.7914 0.1627 9 K 0.0348 0.8299 0.1353 10 S 0.0388 0.8362 0.1249 11 L 0.0456 0.8400 0.1144 12 H 0.0307 0.8726 0.0967 13 L 0.0263 0.8833 0.0904 14 A 0.0278 0.8855 0.0867 15 A 0.0474 0.8630 0.0896 16 V 0.0517 0.8539 0.0945 17 F 0.0653 0.8179 0.1168 18 T 0.0525 0.8000 0.1475 19 C 0.0299 0.8194 0.1507 20 N 0.0237 0.7938 0.1826 21 F 0.0171 0.8367 0.1462 22 T 0.0116 0.8922 0.0962 23 N 0.0095 0.9150 0.0755 24 H 0.0092 0.9194 0.0714 25 M 0.0084 0.9227 0.0689 26 Y 0.0083 0.9238 0.0679 27 A 0.0083 0.9243 0.0675 28 L 0.0083 0.9233 0.0684 29 A 0.0083 0.9235 0.0682 30 A 0.0083 0.9225 0.0692 31 E 0.0083 0.9234 0.0683 32 L 0.0083 0.9221 0.0696 33 L 0.0085 0.9132 0.0783 34 K 0.0090 0.8987 0.0923 35 K 0.0144 0.7951 0.1905 36 Y 0.0583 0.3090 0.6326 37 N 0.0473 0.0838 0.8689 38 L 0.1658 0.0321 0.8021 39 P 0.1642 0.0612 0.7746 40 F 0.0541 0.5544 0.3915 41 D 0.0473 0.6307 0.3221 42 V 0.0552 0.6676 0.2772 43 M 0.0606 0.6567 0.2827 44 L 0.0541 0.7134 0.2325 45 P 0.0150 0.8649 0.1201 46 L 0.0120 0.8803 0.1076 47 I 0.0109 0.8921 0.0970 48 D 0.0092 0.9123 0.0785 49 E 0.0090 0.9071 0.0839 50 T 0.0112 0.9042 0.0845 51 A 0.0089 0.8949 0.0961 52 R 0.0088 0.9052 0.0860 53 K 0.0109 0.8544 0.1347 54 V 0.0177 0.8188 0.1634 55 H 0.0263 0.7350 0.2387 56 E 0.0460 0.5466 0.4074 57 L 0.0985 0.3219 0.5796 58 E 0.1570 0.1027 0.7403 59 P 0.0679 0.4385 0.4936 60 K 0.0813 0.5306 0.3881 61 T 0.1097 0.5107 0.3796 62 A 0.1520 0.4994 0.3487 63 Q 0.1893 0.3392 0.4715 64 T 0.2256 0.1897 0.5847 65 G 0.2429 0.1171 0.6399 66 P 0.1973 0.2961 0.5066 67 A 0.1758 0.4527 0.3714 68 I 0.1992 0.4005 0.4003 69 R 0.1476 0.3907 0.4617 70 Y 0.1208 0.3264 0.5528 71 D 0.1389 0.3387 0.5224 72 E 0.0147 0.7527 0.2326 73 N 0.0121 0.8507 0.1371 74 V 0.0149 0.9014 0.0838 75 I 0.0093 0.9153 0.0754 76 G 0.0090 0.9180 0.0729 77 N 0.0094 0.9070 0.0836 78 H 0.0091 0.9102 0.0806 79 L 0.0090 0.9102 0.0808 80 R 0.0087 0.9004 0.0909 81 M 0.0097 0.8721 0.1182 82 L 0.0176 0.7831 0.1993 83 A 0.0216 0.5606 0.4178 84 D 0.0389 0.3217 0.6394 85 D 0.1270 0.2610 0.6120 86 P 0.0133 0.6963 0.2903 87 A 0.0114 0.7899 0.1987 88 M 0.0107 0.8791 0.1102 89 Q 0.0086 0.9167 0.0747 90 R 0.0083 0.9200 0.0717 91 L 0.0083 0.9228 0.0689 92 Y 0.0083 0.9232 0.0685 93 E 0.0083 0.9236 0.0681 94 L 0.0084 0.9219 0.0697 95 L 0.0088 0.9120 0.0793 96 S 0.0092 0.9051 0.0857 97 R 0.0099 0.8986 0.0915 98 S 0.0164 0.8556 0.1279 99 I 0.0321 0.7625 0.2054 100 H 0.0523 0.6962 0.2515 101 E 0.0942 0.4614 0.4445 102 R 0.1585 0.2403 0.6012 103 Q 0.1593 0.1497 0.6910