# This file is the result of combining several RDB files, specifically # T0473.t04.str2.rdb (weight 1.54425) # T0473.t04.str4.rdb (weight 0.924988) # T0473.t04.pb.rdb (weight 0.789901) # T0473.t04.bys.rdb (weight 0.748322) # T0473.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 T0473.t04.str2.rdb # ============================================ # TARGET T0473 # 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 T0473.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 23.0607 # # ============================================ # Comments from T0473.t04.str4.rdb # ============================================ # TARGET T0473 # 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 T0473.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 23.0607 # # ============================================ # Comments from T0473.t04.pb.rdb # ============================================ # TARGET T0473 # 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 T0473.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 23.0607 # # ============================================ # Comments from T0473.t04.bys.rdb # ============================================ # TARGET T0473 # 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 T0473.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 23.0607 # # ============================================ # Comments from T0473.t04.alpha.rdb # ============================================ # TARGET T0473 # 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 T0473.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 23.0607 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.3721 0.0506 0.5773 2 K 0.4150 0.0459 0.5391 3 I 0.4291 0.0494 0.5215 4 T 0.2276 0.0676 0.7048 5 K 0.0817 0.4288 0.4895 6 D 0.0879 0.3720 0.5400 7 M 0.2492 0.2445 0.5063 8 I 0.2507 0.2718 0.4775 9 I 0.0686 0.7070 0.2244 10 A 0.0296 0.8238 0.1465 11 D 0.0308 0.8626 0.1066 12 V 0.0355 0.8355 0.1290 13 L 0.0456 0.7950 0.1594 14 Q 0.0689 0.6879 0.2432 15 M 0.1083 0.5123 0.3794 16 D 0.1682 0.1490 0.6828 17 R 0.0228 0.5676 0.4097 18 G 0.0236 0.4836 0.4928 19 T 0.0587 0.5229 0.4184 20 A 0.0797 0.6068 0.3135 21 P 0.0619 0.7811 0.1570 22 I 0.0490 0.8521 0.0989 23 F 0.0707 0.8162 0.1131 24 I 0.0517 0.8115 0.1368 25 N 0.0538 0.7088 0.2374 26 N 0.0700 0.2701 0.6599 27 G 0.0553 0.1038 0.8409 28 M 0.1621 0.1256 0.7123 29 H 0.2375 0.1550 0.6076 30 C 0.2376 0.2158 0.5465 31 L 0.1723 0.2187 0.6090 32 G 0.1586 0.1171 0.7243 33 C 0.1951 0.0801 0.7247 34 P 0.1233 0.3286 0.5482 35 S 0.1155 0.4108 0.4737 36 S 0.1163 0.4097 0.4740 37 M 0.0947 0.4024 0.5028 38 G 0.0802 0.4389 0.4809 39 E 0.1178 0.5110 0.3712 40 S 0.1581 0.4884 0.3535 41 I 0.0226 0.7806 0.1968 42 E 0.0099 0.8669 0.1232 43 D 0.0096 0.9063 0.0841 44 A 0.0116 0.9045 0.0839 45 C 0.0144 0.8864 0.0991 46 A 0.0154 0.8665 0.1181 47 V 0.0282 0.7381 0.2337 48 H 0.0637 0.2818 0.6546 49 G 0.0590 0.1395 0.8015 50 I 0.1534 0.1329 0.7136 51 D 0.1802 0.0371 0.7828 52 A 0.0133 0.7219 0.2648 53 D 0.0095 0.8607 0.1297 54 K 0.0084 0.9139 0.0778 55 L 0.0086 0.9112 0.0802 56 V 0.0084 0.9117 0.0799 57 K 0.0083 0.9112 0.0805 58 E 0.0084 0.9140 0.0776 59 L 0.0088 0.9051 0.0860 60 N 0.0087 0.8730 0.1183 61 E 0.0087 0.8545 0.1368 62 Y 0.0103 0.8831 0.1066 63 F 0.0157 0.8514 0.1329 64 E 0.0179 0.8081 0.1740 65 K 0.0382 0.6894 0.2725 66 K 0.0684 0.5150 0.4166 67 E 0.0923 0.3996 0.5081 68 V 0.1303 0.2802 0.5895