# This file is the result of combining several RDB files, specifically # T0480.t06.str2.rdb (weight 1.54425) # T0480.t06.str4.rdb (weight 0.924988) # T0480.t06.pb.rdb (weight 0.789901) # T0480.t06.bys.rdb (weight 0.748322) # T0480.t06.alpha.rdb (weight 0.678173) # T0480.t04.str2.rdb (weight 1.54425) # T0480.t04.str4.rdb (weight 0.924988) # T0480.t04.pb.rdb (weight 0.789901) # T0480.t04.bys.rdb (weight 0.748322) # T0480.t04.alpha.rdb (weight 0.678173) # T0480.t2k.str2.rdb (weight 1.54425) # T0480.t2k.str4.rdb (weight 0.924988) # T0480.t2k.pb.rdb (weight 0.789901) # T0480.t2k.bys.rdb (weight 0.748322) # T0480.t2k.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 T0480.t06.str2.rdb # ============================================ # TARGET T0480 # 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 T0480.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 11.8323 # # ============================================ # Comments from T0480.t06.str4.rdb # ============================================ # TARGET T0480 # 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 T0480.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 11.8323 # # ============================================ # Comments from T0480.t06.pb.rdb # ============================================ # TARGET T0480 # 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 T0480.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 11.8323 # # ============================================ # Comments from T0480.t06.bys.rdb # ============================================ # TARGET T0480 # 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 T0480.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 11.8323 # # ============================================ # Comments from T0480.t06.alpha.rdb # ============================================ # TARGET T0480 # 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 T0480.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 11.8323 # # ============================================ # Comments from T0480.t04.str2.rdb # ============================================ # TARGET T0480 # 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 T0480.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 11.353 # # ============================================ # Comments from T0480.t04.str4.rdb # ============================================ # TARGET T0480 # 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 T0480.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 11.353 # # ============================================ # Comments from T0480.t04.pb.rdb # ============================================ # TARGET T0480 # 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 T0480.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 11.353 # # ============================================ # Comments from T0480.t04.bys.rdb # ============================================ # TARGET T0480 # 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 T0480.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 11.353 # # ============================================ # Comments from T0480.t04.alpha.rdb # ============================================ # TARGET T0480 # 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 T0480.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 11.353 # # ============================================ # Comments from T0480.t2k.str2.rdb # ============================================ # TARGET T0480 # Using neural net dunbrack-40pc-3157-t2k-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 T0480.t2k-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 8.42801 # # ============================================ # Comments from T0480.t2k.str4.rdb # ============================================ # TARGET T0480 # Using neural net dunbrack-40pc-3157-t2k-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 T0480.t2k-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 8.42801 # # ============================================ # Comments from T0480.t2k.pb.rdb # ============================================ # TARGET T0480 # Using neural net dunbrack-40pc-3157-t2k-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 T0480.t2k-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 8.42801 # # ============================================ # Comments from T0480.t2k.bys.rdb # ============================================ # TARGET T0480 # Using neural net dunbrack-40pc-3157-t2k-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 T0480.t2k-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 8.42801 # # ============================================ # Comments from T0480.t2k.alpha.rdb # ============================================ # TARGET T0480 # Using neural net dunbrack-40pc-3157-t2k-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 T0480.t2k-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 8.42801 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.3222 0.1894 0.4884 2 Q 0.3052 0.1682 0.5266 3 K 0.3932 0.1543 0.4526 4 R 0.4737 0.0975 0.4288 5 E 0.5940 0.0523 0.3537 6 L 0.7227 0.0320 0.2453 7 Y 0.7637 0.0123 0.2240 8 E 0.7473 0.0076 0.2451 9 I 0.6444 0.0184 0.3372 10 A 0.4407 0.1171 0.4422 11 D 0.1779 0.0794 0.7427 12 G 0.0890 0.0881 0.8229 13 K 0.4426 0.0235 0.5339 14 L 0.6468 0.0203 0.3329 15 V 0.6719 0.0441 0.2840 16 R 0.6427 0.0721 0.2852 17 K 0.4978 0.1821 0.3201 18 H 0.4275 0.1957 0.3768 19 R 0.2911 0.2317 0.4773 20 F 0.2676 0.1627 0.5697 21 C 0.2214 0.0906 0.6880 22 P 0.1276 0.2704 0.6020 23 R 0.1237 0.2436 0.6327 24 C 0.1518 0.1691 0.6791 25 G 0.1566 0.1308 0.7126 26 P 0.1835 0.2337 0.5828 27 G 0.2766 0.2116 0.5118 28 V 0.4631 0.2278 0.3092 29 F 0.5336 0.1805 0.2860 30 L 0.5223 0.1882 0.2895 31 A 0.4014 0.2488 0.3499 32 E 0.2702 0.2776 0.4523 33 H 0.2253 0.2207 0.5541 34 A 0.1714 0.3373 0.4914 35 D 0.1643 0.3336 0.5021 36 R 0.2009 0.3478 0.4513 37 Y 0.2606 0.2840 0.4554 38 S 0.2900 0.2343 0.4758 39 C 0.2433 0.1905 0.5662 40 G 0.1940 0.1416 0.6644 41 R 0.2626 0.1404 0.5970 42 C 0.2463 0.1380 0.6157 43 G 0.2120 0.1449 0.6430 44 Y 0.3499 0.1849 0.4652 45 T 0.4003 0.2265 0.3732 46 E 0.4037 0.2942 0.3021 47 F 0.3733 0.3392 0.2875 48 K 0.2513 0.4813 0.2673 49 K 0.2214 0.4893 0.2893 50 A 0.1586 0.5111 0.3303 51 K 0.1269 0.4875 0.3856 52 K 0.1502 0.3542 0.4957 53 S 0.1621 0.2490 0.5888 54 K 0.1517 0.2084 0.6400 55 S 0.1604 0.1501 0.6895