# This file is the result of combining several RDB files, specifically # TR469.t2k.str2.rdb (weight 1.54425) # TR469.t2k.str4.rdb (weight 0.924988) # TR469.t2k.pb.rdb (weight 0.789901) # TR469.t2k.bys.rdb (weight 0.748322) # TR469.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 TR469.t2k.str2.rdb # ============================================ # TARGET TR469 # 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 TR469.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 15.0408 # # ============================================ # Comments from TR469.t2k.str4.rdb # ============================================ # TARGET TR469 # 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 TR469.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 15.0408 # # ============================================ # Comments from TR469.t2k.pb.rdb # ============================================ # TARGET TR469 # 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 TR469.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 15.0408 # # ============================================ # Comments from TR469.t2k.bys.rdb # ============================================ # TARGET TR469 # 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 TR469.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 15.0408 # # ============================================ # Comments from TR469.t2k.alpha.rdb # ============================================ # TARGET TR469 # 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 TR469.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 15.0408 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 Q 0.3834 0.1393 0.4772 2 K 0.4338 0.0897 0.4764 3 F 0.4390 0.0832 0.4778 4 T 0.2464 0.0642 0.6894 5 K 0.1023 0.4038 0.4939 6 D 0.0929 0.3483 0.5589 7 M 0.2164 0.2576 0.5260 8 T 0.1975 0.3275 0.4749 9 F 0.0596 0.7323 0.2081 10 A 0.0223 0.8535 0.1243 11 Q 0.0168 0.9035 0.0797 12 A 0.0159 0.8887 0.0955 13 L 0.0202 0.8613 0.1185 14 Q 0.0231 0.7704 0.2065 15 T 0.0482 0.5789 0.3729 16 H 0.1340 0.2178 0.6482 17 P 0.0313 0.6010 0.3677 18 G 0.0229 0.5815 0.3957 19 V 0.0330 0.7620 0.2051 20 A 0.0221 0.8583 0.1196 21 G 0.0156 0.8923 0.0921 22 V 0.0169 0.8991 0.0841 23 L 0.0185 0.8853 0.0961 24 R 0.0195 0.8528 0.1277 25 S 0.0306 0.7387 0.2306 26 Y 0.0658 0.3661 0.5681 27 N 0.0778 0.1753 0.7470 28 L 0.1666 0.1790 0.6544 29 G 0.1942 0.1639 0.6419 30 C 0.2512 0.2083 0.5405 31 I 0.2239 0.2119 0.5642 32 G 0.1951 0.1492 0.6557 33 C 0.2163 0.1566 0.6272 34 M 0.1312 0.3615 0.5073 35 G 0.1060 0.3766 0.5174 36 A 0.1170 0.3995 0.4835 37 Q 0.0852 0.4132 0.5016 38 N 0.0790 0.4999 0.4211 39 E 0.0809 0.6251 0.2940 40 S 0.0809 0.6399 0.2791 41 L 0.0164 0.7951 0.1885 42 E 0.0098 0.8859 0.1043 43 Q 0.0117 0.9052 0.0830 44 G 0.0158 0.8936 0.0906 45 A 0.0166 0.8777 0.1057 46 N 0.0206 0.8232 0.1562 47 A 0.0277 0.7165 0.2557 48 H 0.0634 0.2475 0.6891 49 G 0.0540 0.0997 0.8463 50 L 0.1871 0.0680 0.7450 51 N 0.1750 0.0402 0.7847 52 V 0.0125 0.7400 0.2474 53 E 0.0092 0.8722 0.1186 54 D 0.0088 0.9188 0.0724 55 I 0.0086 0.9214 0.0699 56 L 0.0083 0.9189 0.0727 57 R 0.0083 0.9127 0.0790 58 D 0.0090 0.8681 0.1229 59 L 0.0136 0.8439 0.1424 60 N 0.0126 0.7445 0.2429 61 A 0.0176 0.6770 0.3054 62 L 0.0452 0.5288 0.4260 63 A 0.0821 0.3903 0.5276