# 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) # 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 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.2768 0.1643 0.5588 2 Q 0.3590 0.1531 0.4879 3 K 0.5047 0.1376 0.3577 4 R 0.5788 0.1025 0.3187 5 E 0.6879 0.0624 0.2497 6 L 0.7377 0.0309 0.2314 7 Y 0.7574 0.0186 0.2240 8 E 0.7487 0.0135 0.2379 9 I 0.6678 0.0296 0.3027 10 A 0.4636 0.1456 0.3908 11 D 0.1840 0.0874 0.7286 12 G 0.1367 0.0865 0.7768 13 K 0.5278 0.0262 0.4460 14 L 0.6430 0.0212 0.3358 15 V 0.6315 0.0551 0.3134 16 R 0.6490 0.0735 0.2775 17 K 0.5266 0.1664 0.3070 18 H 0.4439 0.1854 0.3707 19 R 0.3237 0.2337 0.4427 20 F 0.2638 0.1884 0.5478 21 C 0.2228 0.0825 0.6947 22 P 0.1004 0.2898 0.6098 23 R 0.1177 0.2626 0.6197 24 C 0.1405 0.1657 0.6938 25 G 0.1513 0.1178 0.7309 26 P 0.1410 0.2282 0.6308 27 G 0.2175 0.2262 0.5563 28 V 0.4628 0.2043 0.3330 29 F 0.5852 0.1639 0.2509 30 L 0.5241 0.2246 0.2513 31 A 0.4465 0.2659 0.2876 32 E 0.3207 0.3359 0.3434 33 H 0.2280 0.2860 0.4860 34 A 0.1248 0.3420 0.5332 35 D 0.1245 0.3316 0.5439 36 R 0.1772 0.3338 0.4889 37 Y 0.2705 0.3004 0.4291 38 S 0.3051 0.2238 0.4711 39 C 0.3008 0.1429 0.5563 40 G 0.2402 0.1195 0.6403 41 R 0.3649 0.1252 0.5099 42 C 0.3479 0.1099 0.5422 43 G 0.3554 0.1159 0.5287 44 Y 0.4966 0.1320 0.3714 45 T 0.5564 0.1502 0.2933 46 E 0.5551 0.1953 0.2496 47 F 0.4830 0.2459 0.2711 48 K 0.4141 0.2931 0.2928 49 K 0.3356 0.2917 0.3727 50 A 0.2025 0.3499 0.4477 51 K 0.1299 0.3716 0.4985 52 K 0.1416 0.3371 0.5213 53 S 0.1677 0.2577 0.5745 54 K 0.1683 0.2178 0.6138 55 S 0.1843 0.1661 0.6496