# This file is the result of combining several RDB files, specifically # T0397.t2k.str2.rdb (weight 1.54425) # T0397.t2k.str4.rdb (weight 0.924988) # T0397.t2k.pb.rdb (weight 0.789901) # T0397.t2k.bys.rdb (weight 0.748322) # T0397.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 T0397.t2k.str2.rdb # ============================================ # TARGET T0397 # 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 T0397.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 3.24605 # # ============================================ # Comments from T0397.t2k.str4.rdb # ============================================ # TARGET T0397 # 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 T0397.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 3.24605 # # ============================================ # Comments from T0397.t2k.pb.rdb # ============================================ # TARGET T0397 # 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 T0397.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 3.24605 # # ============================================ # Comments from T0397.t2k.bys.rdb # ============================================ # TARGET T0397 # 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 T0397.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 3.24605 # # ============================================ # Comments from T0397.t2k.alpha.rdb # ============================================ # TARGET T0397 # 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 T0397.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 3.24605 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.3565 0.0596 0.5838 2 K 0.3624 0.0386 0.5990 3 I 0.3935 0.0196 0.5869 4 P 0.3513 0.0329 0.6157 5 K 0.6372 0.0251 0.3377 6 I 0.7458 0.0103 0.2439 7 Y 0.7800 0.0079 0.2121 8 V 0.7161 0.0155 0.2684 9 E 0.5896 0.0415 0.3689 10 G 0.4122 0.0564 0.5314 11 E 0.4158 0.0714 0.5128 12 L 0.3889 0.0993 0.5118 13 N 0.2686 0.1102 0.6212 14 D 0.1482 0.1347 0.7172 15 G 0.0775 0.1154 0.8070 16 D 0.2208 0.0924 0.6868 17 R 0.4676 0.0399 0.4924 18 V 0.6558 0.0310 0.3132 19 A 0.7062 0.0283 0.2655 20 I 0.6878 0.0412 0.2710 21 E 0.5366 0.0904 0.3730 22 K 0.3526 0.1469 0.5006 23 D 0.1794 0.1031 0.7175 24 G 0.1798 0.0753 0.7448 25 N 0.4922 0.0378 0.4700 26 A 0.7054 0.0250 0.2696 27 I 0.7320 0.0278 0.2401 28 I 0.7354 0.0340 0.2306 29 F 0.6500 0.0507 0.2993 30 L 0.4744 0.1327 0.3928 31 E 0.3364 0.1976 0.4660 32 K 0.2540 0.2517 0.4943 33 D 0.2066 0.3007 0.4927 34 E 0.1383 0.4774 0.3843 35 E 0.1826 0.3710 0.4464 36 Y 0.2509 0.2082 0.5409 37 S 0.1884 0.1448 0.6668 38 G 0.1351 0.1506 0.7143 39 N 0.1442 0.1355 0.7202 40 G 0.2064 0.0787 0.7150 41 K 0.5637 0.0221 0.4143 42 L 0.7020 0.0142 0.2838 43 L 0.7250 0.0223 0.2528 44 Y 0.7850 0.0191 0.1958 45 Q 0.7739 0.0191 0.2070 46 V 0.7654 0.0236 0.2110 47 I 0.6702 0.0631 0.2668 48 Y 0.4484 0.1879 0.3637 49 D 0.2433 0.3490 0.4077 50 D 0.1608 0.4022 0.4370 51 L 0.0437 0.6745 0.2819 52 A 0.0263 0.7827 0.1910 53 K 0.0339 0.7778 0.1883 54 Y 0.0812 0.6897 0.2291 55 M 0.1994 0.5289 0.2718 56 S 0.1896 0.4495 0.3609 57 L 0.0899 0.5535 0.3565 58 D 0.0758 0.5022 0.4221 59 T 0.1524 0.3670 0.4806 60 L 0.2632 0.2371 0.4998 61 K 0.2955 0.1554 0.5491 62 K 0.3290 0.1888 0.4822 63 D 0.4129 0.0981 0.4890 64 V 0.6966 0.0281 0.2754 65 L 0.7520 0.0160 0.2320 66 I 0.7737 0.0124 0.2139 67 Q 0.6789 0.0173 0.3038 68 Y 0.3703 0.0182 0.6115 69 P 0.1737 0.1561 0.6701 70 D 0.1065 0.1956 0.6979 71 K 0.1345 0.1567 0.7087 72 H 0.3384 0.0846 0.5770 73 T 0.5961 0.0439 0.3600 74 L 0.6950 0.0337 0.2712 75 T 0.7343 0.0334 0.2323 76 Y 0.7458 0.0359 0.2183 77 L 0.6744 0.0647 0.2609 78 K 0.5014 0.1065 0.3920 79 A 0.2760 0.1274 0.5966 80 G 0.1414 0.0955 0.7631 81 T 0.2081 0.0760 0.7159 82 K 0.1872 0.1753 0.6375