# 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 R 0.2724 0.0388 0.6888 2 P 0.2841 0.0949 0.6210 3 W 0.3831 0.1182 0.4987 4 R 0.5586 0.0681 0.3733 5 L 0.6729 0.0418 0.2853 6 E 0.7396 0.0261 0.2343 7 V 0.7684 0.0167 0.2149 8 V 0.7276 0.0224 0.2500 9 L 0.6529 0.0275 0.3195 10 D 0.4112 0.0213 0.5675 11 P 0.2547 0.0526 0.6927 12 P 0.2120 0.0417 0.7463 13 P 0.1228 0.1656 0.7115 14 G 0.0946 0.1328 0.7726 15 R 0.1307 0.2861 0.5832 16 E 0.1055 0.4746 0.4198 17 E 0.1469 0.4736 0.3795 18 V 0.1688 0.4849 0.3463 19 Y 0.1245 0.5746 0.3008 20 P 0.0495 0.7917 0.1588 21 L 0.0230 0.8679 0.1091 22 L 0.0156 0.8973 0.0871 23 A 0.0139 0.9032 0.0830 24 Q 0.0140 0.9029 0.0832 25 V 0.0168 0.8891 0.0941 26 A 0.0202 0.8623 0.1175 27 R 0.0321 0.8081 0.1598 28 R 0.0575 0.6316 0.3109 29 A 0.0929 0.2994 0.6077 30 G 0.0896 0.1244 0.7860 31 G 0.2117 0.0634 0.7249 32 V 0.5085 0.0291 0.4624 33 T 0.6638 0.0245 0.3117 34 V 0.7058 0.0257 0.2685 35 R 0.6316 0.0380 0.3303 36 M 0.4219 0.0913 0.4868 37 G 0.2283 0.0996 0.6722 38 D 0.1747 0.1553 0.6700 39 G 0.1445 0.1916 0.6640 40 L 0.2292 0.2411 0.5297 41 A 0.2429 0.2551 0.5020 42 S 0.2341 0.2157 0.5502 43 W 0.2376 0.1286 0.6338 44 S 0.2371 0.0465 0.7164 45 P 0.1959 0.0763 0.7279 46 P 0.1520 0.2749 0.5731 47 E 0.3022 0.2395 0.4583 48 V 0.6434 0.0757 0.2808 49 L 0.6888 0.0627 0.2485 50 V 0.7128 0.0568 0.2303 51 L 0.5665 0.1144 0.3191 52 E 0.3281 0.1940 0.4779 53 G 0.2112 0.2064 0.5824 54 T 0.2203 0.3874 0.3923 55 L 0.1713 0.5731 0.2556 56 A 0.1170 0.6343 0.2487 57 R 0.1234 0.5458 0.3308 58 M 0.1350 0.3442 0.5208 59 G 0.1186 0.2223 0.6591 60 Q 0.2380 0.2626 0.4994 61 T 0.3268 0.2746 0.3986 62 Y 0.3737 0.2845 0.3418 63 A 0.4561 0.2429 0.3010 64 Y 0.5049 0.2122 0.2828 65 R 0.5469 0.1492 0.3039 66 L 0.5279 0.1051 0.3670 67 Y 0.3645 0.0443 0.5912 68 P 0.2195 0.1806 0.5999 69 K 0.0986 0.2146 0.6868 70 G 0.0947 0.1328 0.7725 71 R 0.2051 0.0857 0.7093 72 R 0.2836 0.0362 0.6802 73 P 0.2586 0.0694 0.6720 74 L 0.2135 0.1352 0.6513