# This file is the result of combining several RDB files, specifically # T0499.t2k.str2.rdb (weight 1.54425) # T0499.t2k.str4.rdb (weight 0.924988) # T0499.t2k.pb.rdb (weight 0.789901) # T0499.t2k.bys.rdb (weight 0.748322) # T0499.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 T0499.t2k.str2.rdb # ============================================ # TARGET T0499 # 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 T0499.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 3.86358 # # ============================================ # Comments from T0499.t2k.str4.rdb # ============================================ # TARGET T0499 # 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 T0499.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 3.86358 # # ============================================ # Comments from T0499.t2k.pb.rdb # ============================================ # TARGET T0499 # 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 T0499.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 3.86358 # # ============================================ # Comments from T0499.t2k.bys.rdb # ============================================ # TARGET T0499 # 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 T0499.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 3.86358 # # ============================================ # Comments from T0499.t2k.alpha.rdb # ============================================ # TARGET T0499 # 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 T0499.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 3.86358 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 T 0.4553 0.0663 0.4784 2 T 0.5898 0.0454 0.3648 3 Y 0.7233 0.0275 0.2492 4 K 0.7831 0.0154 0.2015 5 L 0.7865 0.0123 0.2013 6 I 0.7773 0.0206 0.2021 7 L 0.7233 0.0437 0.2330 8 N 0.5651 0.0608 0.3741 9 L 0.3105 0.1999 0.4895 10 K 0.2168 0.3038 0.4794 11 Q 0.2343 0.2906 0.4751 12 A 0.1988 0.3410 0.4602 13 K 0.1607 0.4518 0.3876 14 E 0.1209 0.6102 0.2689 15 E 0.1236 0.6550 0.2214 16 A 0.1580 0.6102 0.2318 17 I 0.1307 0.6325 0.2368 18 K 0.1013 0.6839 0.2148 19 E 0.0882 0.6836 0.2282 20 A 0.1073 0.6355 0.2572 21 V 0.1479 0.5652 0.2868 22 D 0.1240 0.4986 0.3773 23 A 0.0199 0.7533 0.2268 24 G 0.0143 0.7858 0.1999 25 T 0.0168 0.8285 0.1547 26 A 0.0095 0.8963 0.0941 27 E 0.0085 0.9154 0.0761 28 K 0.0084 0.9194 0.0722 29 Y 0.0087 0.9144 0.0769 30 F 0.0089 0.9143 0.0768 31 K 0.0090 0.9141 0.0769 32 L 0.0114 0.8975 0.0911 33 I 0.0287 0.8142 0.1571 34 A 0.0531 0.6706 0.2763 35 N 0.0788 0.4313 0.4898 36 A 0.0649 0.3272 0.6078 37 K 0.0689 0.1937 0.7374 38 T 0.1560 0.0816 0.7624 39 V 0.3354 0.0667 0.5979 40 E 0.4161 0.0836 0.5003 41 G 0.4716 0.0646 0.4637 42 V 0.6231 0.0409 0.3360 43 W 0.6772 0.0324 0.2904 44 T 0.6323 0.0406 0.3271 45 Y 0.5029 0.0839 0.4132 46 K 0.2389 0.2954 0.4657 47 D 0.1633 0.3623 0.4744 48 E 0.2112 0.3599 0.4290 49 I 0.3499 0.2371 0.4130 50 K 0.3980 0.1499 0.4521 51 T 0.5021 0.0735 0.4244 52 F 0.5358 0.0418 0.4224 53 T 0.5977 0.0292 0.3731 54 V 0.5180 0.0604 0.4216 55 T 0.3539 0.0594 0.5867 56 E 0.2556 0.2234 0.5210