# This file is the result of combining several RDB files, specifically # T0472.t06.str2.rdb (weight 1.54425) # T0472.t06.str4.rdb (weight 0.924988) # T0472.t06.pb.rdb (weight 0.789901) # T0472.t06.bys.rdb (weight 0.748322) # T0472.t06.alpha.rdb (weight 0.678173) # T0472.t04.str2.rdb (weight 1.54425) # T0472.t04.str4.rdb (weight 0.924988) # T0472.t04.pb.rdb (weight 0.789901) # T0472.t04.bys.rdb (weight 0.748322) # T0472.t04.alpha.rdb (weight 0.678173) # T0472.t2k.str2.rdb (weight 1.54425) # T0472.t2k.str4.rdb (weight 0.924988) # T0472.t2k.pb.rdb (weight 0.789901) # T0472.t2k.bys.rdb (weight 0.748322) # T0472.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 T0472.t06.str2.rdb # ============================================ # TARGET T0472 # 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 T0472.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 20.6079 # # ============================================ # Comments from T0472.t06.str4.rdb # ============================================ # TARGET T0472 # 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 T0472.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 20.6079 # # ============================================ # Comments from T0472.t06.pb.rdb # ============================================ # TARGET T0472 # 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 T0472.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 20.6079 # # ============================================ # Comments from T0472.t06.bys.rdb # ============================================ # TARGET T0472 # 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 T0472.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 20.6079 # # ============================================ # Comments from T0472.t06.alpha.rdb # ============================================ # TARGET T0472 # 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 T0472.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 20.6079 # # ============================================ # Comments from T0472.t04.str2.rdb # ============================================ # TARGET T0472 # 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 T0472.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 20.0586 # # ============================================ # Comments from T0472.t04.str4.rdb # ============================================ # TARGET T0472 # 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 T0472.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 20.0586 # # ============================================ # Comments from T0472.t04.pb.rdb # ============================================ # TARGET T0472 # 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 T0472.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 20.0586 # # ============================================ # Comments from T0472.t04.bys.rdb # ============================================ # TARGET T0472 # 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 T0472.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 20.0586 # # ============================================ # Comments from T0472.t04.alpha.rdb # ============================================ # TARGET T0472 # 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 T0472.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 20.0586 # # ============================================ # Comments from T0472.t2k.str2.rdb # ============================================ # TARGET T0472 # 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 T0472.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 12.7033 # # ============================================ # Comments from T0472.t2k.str4.rdb # ============================================ # TARGET T0472 # 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 T0472.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 12.7033 # # ============================================ # Comments from T0472.t2k.pb.rdb # ============================================ # TARGET T0472 # 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 T0472.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 12.7033 # # ============================================ # Comments from T0472.t2k.bys.rdb # ============================================ # TARGET T0472 # 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 T0472.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 12.7033 # # ============================================ # Comments from T0472.t2k.alpha.rdb # ============================================ # TARGET T0472 # 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 T0472.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 12.7033 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 P 0.1848 0.1303 0.6849 2 I 0.1361 0.3446 0.5193 3 E 0.1164 0.4893 0.3943 4 A 0.1178 0.5696 0.3125 5 R 0.1519 0.5664 0.2818 6 Y 0.2514 0.5023 0.2463 7 A 0.3458 0.4195 0.2348 8 K 0.4427 0.3273 0.2299 9 E 0.4343 0.2830 0.2827 10 V 0.4238 0.2469 0.3293 11 A 0.2782 0.2337 0.4881 12 K 0.1379 0.2682 0.5939 13 N 0.0881 0.1618 0.7500 14 D 0.0778 0.1064 0.8157 15 K 0.3151 0.0204 0.6644 16 P 0.5933 0.0211 0.3856 17 Y 0.7317 0.0171 0.2511 18 F 0.7922 0.0078 0.2000 19 N 0.7868 0.0070 0.2062 20 L 0.7750 0.0106 0.2144 21 K 0.6519 0.0330 0.3151 22 A 0.4188 0.0640 0.5173 23 A 0.2428 0.1260 0.6312 24 N 0.1615 0.1016 0.7369 25 H 0.1940 0.1311 0.6749 26 Q 0.4848 0.0547 0.4605 27 I 0.6573 0.0277 0.3150 28 I 0.6834 0.0391 0.2775 29 G 0.6172 0.0550 0.3277 30 T 0.4897 0.1247 0.3856 31 S 0.3546 0.1791 0.4664 32 Q 0.2089 0.3654 0.4257 33 M 0.1864 0.4090 0.4045 34 Y 0.2088 0.3745 0.4167 35 S 0.1707 0.3943 0.4350 36 S 0.1341 0.4495 0.4164 37 T 0.0201 0.7615 0.2184 38 A 0.0209 0.7932 0.1859 39 A 0.0228 0.8219 0.1552 40 R 0.0231 0.8089 0.1680 41 D 0.0366 0.6573 0.3062 42 N 0.0526 0.3079 0.6395 43 G 0.0644 0.1726 0.7630 44 I 0.1644 0.3822 0.4534 45 K 0.2120 0.4863 0.3017 46 S 0.2035 0.5766 0.2199 47 V 0.1583 0.6573 0.1844 48 M 0.1498 0.6135 0.2367 49 E 0.1093 0.4772 0.4135 50 N 0.0997 0.2377 0.6627 51 G 0.1288 0.1700 0.7012 52 K 0.1211 0.2364 0.6425 53 T 0.1562 0.2063 0.6375 54 T 0.2418 0.1841 0.5741 55 T 0.3862 0.1586 0.4552 56 I 0.3793 0.2408 0.3799 57 K 0.3385 0.2577 0.4038 58 D 0.2763 0.2056 0.5180 59 L 0.2002 0.2127 0.5871 60 T 0.1724 0.1304 0.6972