# This file is the result of combining several RDB files, specifically # 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) # 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.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 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.2674 0.1548 0.5778 2 Q 0.3527 0.1350 0.5123 3 K 0.4930 0.1391 0.3678 4 R 0.5471 0.1107 0.3422 5 E 0.6367 0.0740 0.2893 6 L 0.7019 0.0386 0.2595 7 Y 0.7427 0.0147 0.2426 8 E 0.7432 0.0106 0.2462 9 I 0.6622 0.0231 0.3147 10 A 0.3694 0.1017 0.5289 11 D 0.1265 0.1120 0.7615 12 G 0.0711 0.1053 0.8235 13 K 0.5002 0.0233 0.4765 14 L 0.6468 0.0173 0.3359 15 V 0.6337 0.0481 0.3182 16 R 0.6573 0.0641 0.2787 17 K 0.4778 0.1561 0.3661 18 H 0.3878 0.1961 0.4161 19 R 0.3605 0.1983 0.4412 20 F 0.3091 0.1579 0.5329 21 C 0.2292 0.0878 0.6830 22 P 0.1026 0.3431 0.5543 23 R 0.1094 0.2765 0.6140 24 C 0.1579 0.1622 0.6799 25 G 0.1451 0.0929 0.7620 26 P 0.1471 0.2391 0.6138 27 G 0.2464 0.1851 0.5685 28 V 0.4712 0.2013 0.3275 29 F 0.5415 0.1960 0.2625 30 L 0.5481 0.2068 0.2451 31 A 0.4149 0.3180 0.2671 32 E 0.2750 0.3665 0.3585 33 H 0.2035 0.3314 0.4651 34 A 0.1424 0.3444 0.5133 35 D 0.1229 0.3142 0.5629 36 R 0.1363 0.3525 0.5113 37 Y 0.2048 0.2848 0.5103 38 S 0.2238 0.2755 0.5007 39 C 0.2430 0.1719 0.5852 40 G 0.2109 0.1521 0.6371 41 R 0.2704 0.1766 0.5530 42 C 0.3224 0.1265 0.5512 43 G 0.3357 0.1346 0.5298 44 Y 0.4820 0.1496 0.3683 45 T 0.5460 0.1626 0.2915 46 E 0.5766 0.1819 0.2414 47 F 0.4818 0.2830 0.2351 48 K 0.4028 0.3591 0.2381 49 K 0.3054 0.3722 0.3223 50 A 0.1757 0.4401 0.3842 51 K 0.1189 0.4734 0.4077 52 K 0.1225 0.4441 0.4334 53 S 0.1611 0.3215 0.5173 54 K 0.1654 0.2580 0.5765 55 S 0.1838 0.1789 0.6374