# This file is the result of combining several RDB files, specifically # T0492.t06.str2.rdb (weight 1.54425) # T0492.t06.str4.rdb (weight 0.924988) # T0492.t06.pb.rdb (weight 0.789901) # T0492.t06.bys.rdb (weight 0.748322) # T0492.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 T0492.t06.str2.rdb # ============================================ # TARGET T0492 # 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 T0492.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 61.5359 # # ============================================ # Comments from T0492.t06.str4.rdb # ============================================ # TARGET T0492 # 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 T0492.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 61.5359 # # ============================================ # Comments from T0492.t06.pb.rdb # ============================================ # TARGET T0492 # 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 T0492.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 61.5359 # # ============================================ # Comments from T0492.t06.bys.rdb # ============================================ # TARGET T0492 # 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 T0492.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 61.5359 # # ============================================ # Comments from T0492.t06.alpha.rdb # ============================================ # TARGET T0492 # 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 T0492.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 61.5359 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.3190 0.0896 0.5914 2 F 0.3949 0.0369 0.5682 3 S 0.3032 0.0376 0.6592 4 L 0.1313 0.4177 0.4510 5 R 0.0842 0.5378 0.3781 6 D 0.1071 0.4153 0.4776 7 A 0.2312 0.1381 0.6307 8 K 0.2009 0.1380 0.6611 9 C 0.1298 0.1407 0.7296 10 G 0.0720 0.0860 0.8420 11 Q 0.3080 0.0298 0.6622 12 T 0.6257 0.0167 0.3576 13 V 0.7495 0.0078 0.2427 14 K 0.7984 0.0062 0.1954 15 V 0.7378 0.0060 0.2562 16 V 0.7038 0.0135 0.2827 17 K 0.7607 0.0103 0.2290 18 L 0.6416 0.0254 0.3330 19 H 0.4584 0.0546 0.4869 20 G 0.2668 0.1024 0.6308 21 T 0.1056 0.2527 0.6417 22 G 0.0524 0.4052 0.5424 23 A 0.0428 0.7210 0.2362 24 L 0.0312 0.8415 0.1273 25 K 0.0160 0.8917 0.0923 26 R 0.0123 0.9088 0.0789 27 R 0.0123 0.9000 0.0877 28 I 0.0172 0.8875 0.0953 29 M 0.0311 0.8419 0.1270 30 D 0.0549 0.6684 0.2767 31 M 0.1115 0.2977 0.5908 32 G 0.1586 0.1321 0.7092 33 I 0.3727 0.0646 0.5627 34 T 0.3595 0.0603 0.5802 35 R 0.1548 0.1538 0.6914 36 G 0.0741 0.1011 0.8248 37 C 0.4277 0.0258 0.5465 38 E 0.6777 0.0135 0.3088 39 I 0.7805 0.0071 0.2124 40 Y 0.7835 0.0080 0.2085 41 I 0.7560 0.0075 0.2365 42 R 0.7394 0.0229 0.2377 43 K 0.7263 0.0228 0.2508 44 V 0.6170 0.0436 0.3394 45 A 0.3865 0.0284 0.5851 46 P 0.2672 0.1228 0.6101 47 L 0.1309 0.1671 0.7020 48 G 0.0890 0.0843 0.8267 49 D 0.2260 0.0251 0.7488 50 P 0.4008 0.0412 0.5579 51 I 0.6798 0.0421 0.2781 52 Q 0.7813 0.0098 0.2089 53 I 0.8041 0.0076 0.1883 54 N 0.7761 0.0077 0.2162 55 V 0.6834 0.0175 0.2991 56 R 0.3401 0.0682 0.5917 57 G 0.2157 0.0551 0.7293 58 Y 0.4740 0.0502 0.4758 59 E 0.6693 0.0696 0.2612 60 L 0.6543 0.1153 0.2305 61 S 0.6192 0.1375 0.2433 62 L 0.5222 0.1855 0.2924 63 R 0.3199 0.2293 0.4508 64 K 0.0862 0.5985 0.3152 65 S 0.0507 0.6818 0.2675 66 A 0.0438 0.6981 0.2581 67 A 0.0808 0.6657 0.2535 68 E 0.1004 0.5427 0.3569 69 M 0.2610 0.3025 0.4365 70 I 0.5280 0.0720 0.3999 71 E 0.5921 0.0457 0.3622 72 V 0.6121 0.0383 0.3497 73 E 0.4153 0.0646 0.5201