# This file is the result of combining several RDB files, specifically # T0462.t06.str2.rdb (weight 1.54425) # T0462.t06.str4.rdb (weight 0.924988) # T0462.t06.pb.rdb (weight 0.789901) # T0462.t06.bys.rdb (weight 0.748322) # T0462.t06.alpha.rdb (weight 0.678173) # T0462.t04.str2.rdb (weight 1.54425) # T0462.t04.str4.rdb (weight 0.924988) # T0462.t04.pb.rdb (weight 0.789901) # T0462.t04.bys.rdb (weight 0.748322) # T0462.t04.alpha.rdb (weight 0.678173) # T0462.t2k.str2.rdb (weight 1.54425) # T0462.t2k.str4.rdb (weight 0.924988) # T0462.t2k.pb.rdb (weight 0.789901) # T0462.t2k.bys.rdb (weight 0.748322) # T0462.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 T0462.t06.str2.rdb # ============================================ # TARGET T0462 # 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 T0462.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 T0462.t06.str4.rdb # ============================================ # TARGET T0462 # 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 T0462.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 T0462.t06.pb.rdb # ============================================ # TARGET T0462 # 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 T0462.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 T0462.t06.bys.rdb # ============================================ # TARGET T0462 # 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 T0462.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 T0462.t06.alpha.rdb # ============================================ # TARGET T0462 # 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 T0462.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 T0462.t04.str2.rdb # ============================================ # TARGET T0462 # 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 T0462.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 1 # # ============================================ # Comments from T0462.t04.str4.rdb # ============================================ # TARGET T0462 # 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 T0462.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 1 # # ============================================ # Comments from T0462.t04.pb.rdb # ============================================ # TARGET T0462 # 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 T0462.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 1 # # ============================================ # Comments from T0462.t04.bys.rdb # ============================================ # TARGET T0462 # 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 T0462.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 1 # # ============================================ # Comments from T0462.t04.alpha.rdb # ============================================ # TARGET T0462 # 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 T0462.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 1 # # ============================================ # Comments from T0462.t2k.str2.rdb # ============================================ # TARGET T0462 # 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 T0462.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 5 # # ============================================ # Comments from T0462.t2k.str4.rdb # ============================================ # TARGET T0462 # 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 T0462.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 5 # # ============================================ # Comments from T0462.t2k.pb.rdb # ============================================ # TARGET T0462 # 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 T0462.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 5 # # ============================================ # Comments from T0462.t2k.bys.rdb # ============================================ # TARGET T0462 # 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 T0462.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 5 # # ============================================ # Comments from T0462.t2k.alpha.rdb # ============================================ # TARGET T0462 # 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 T0462.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 5 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 G 0.0975 0.0802 0.8223 2 G 0.1489 0.0764 0.7747 3 E 0.3931 0.0613 0.5457 4 L 0.5585 0.0232 0.4183 5 P 0.5260 0.0245 0.4495 6 L 0.6795 0.0258 0.2947 7 I 0.7035 0.0275 0.2690 8 L 0.6726 0.0297 0.2977 9 A 0.4671 0.0509 0.4820 10 D 0.2868 0.1531 0.5601 11 D 0.1699 0.1045 0.7256 12 G 0.2215 0.0666 0.7119 13 T 0.5952 0.0203 0.3845 14 Y 0.7268 0.0094 0.2638 15 E 0.7902 0.0079 0.2019 16 I 0.7714 0.0071 0.2215 17 T 0.7693 0.0139 0.2168 18 K 0.7553 0.0158 0.2288 19 L 0.5694 0.0623 0.3683 20 N 0.2909 0.1110 0.5981 21 G 0.1437 0.1749 0.6814 22 G 0.1090 0.3793 0.5117 23 R 0.0675 0.6671 0.2653 24 R 0.0465 0.7854 0.1681 25 F 0.0380 0.8485 0.1135 26 L 0.0192 0.8949 0.0859 27 F 0.0153 0.9034 0.0813 28 R 0.0176 0.8913 0.0911 29 M 0.0251 0.8689 0.1060 30 K 0.0233 0.8514 0.1253 31 N 0.0668 0.6835 0.2497 32 L 0.0938 0.3355 0.5706 33 G 0.1625 0.1172 0.7203 34 I 0.3336 0.0879 0.5785 35 E 0.4060 0.1068 0.4872 36 S 0.3023 0.0898 0.6079 37 G 0.1909 0.0638 0.7454 38 K 0.4508 0.0287 0.5206 39 K 0.7065 0.0125 0.2810 40 I 0.7735 0.0080 0.2185 41 Q 0.7435 0.0066 0.2499 42 V 0.6893 0.0115 0.2992 43 S 0.5024 0.0375 0.4601 44 G 0.3266 0.0451 0.6283 45 R 0.4013 0.0489 0.5499 46 R 0.6238 0.0221 0.3540 47 Y 0.7298 0.0104 0.2599 48 Y 0.7422 0.0085 0.2493 49 I 0.6562 0.0214 0.3224 50 E 0.4012 0.0459 0.5528 51 G 0.2336 0.0620 0.7045 52 R 0.3753 0.0772 0.5476 53 E 0.6160 0.0404 0.3436 54 I 0.6813 0.0320 0.2867 55 D 0.6291 0.0345 0.3364 56 L 0.5031 0.0860 0.4110 57 G 0.2969 0.0850 0.6181 58 Y 0.2372 0.1377 0.6251 59 G 0.1775 0.1312 0.6913 60 E 0.2822 0.2026 0.5152 61 A 0.3676 0.2042 0.4282 62 T 0.4308 0.1581 0.4111 63 K 0.6255 0.0657 0.3089 64 I 0.7167 0.0281 0.2553 65 W 0.7533 0.0268 0.2199 66 V 0.7259 0.0434 0.2306 67 R 0.6748 0.0603 0.2649 68 R 0.5863 0.0604 0.3533 69 V 0.3930 0.1606 0.4464 70 S 0.2452 0.2087 0.5462 71 D 0.1459 0.3062 0.5479 72 A 0.1048 0.2621 0.6331 73 G 0.0956 0.1863 0.7181 74 E 0.1526 0.2994 0.5480 75 E 0.1750 0.2989 0.5261 76 S 0.2021 0.1987 0.5992 77 H 0.2279 0.0812 0.6909 78 P 0.1543 0.2221 0.6236 79 Q 0.1724 0.2081 0.6194 80 K 0.1827 0.1694 0.6479