# This file is the result of combining several RDB files, specifically # TR453.t06.str2.rdb (weight 1.54425) # TR453.t06.str4.rdb (weight 0.924988) # TR453.t06.pb.rdb (weight 0.789901) # TR453.t06.bys.rdb (weight 0.748322) # TR453.t06.alpha.rdb (weight 0.678173) # TR453.t04.str2.rdb (weight 1.54425) # TR453.t04.str4.rdb (weight 0.924988) # TR453.t04.pb.rdb (weight 0.789901) # TR453.t04.bys.rdb (weight 0.748322) # TR453.t04.alpha.rdb (weight 0.678173) # TR453.t2k.str2.rdb (weight 1.54425) # TR453.t2k.str4.rdb (weight 0.924988) # TR453.t2k.pb.rdb (weight 0.789901) # TR453.t2k.bys.rdb (weight 0.748322) # TR453.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 TR453.t06.str2.rdb # ============================================ # TARGET TR453 # 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 TR453.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 136.399 # # ============================================ # Comments from TR453.t06.str4.rdb # ============================================ # TARGET TR453 # 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 TR453.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 136.399 # # ============================================ # Comments from TR453.t06.pb.rdb # ============================================ # TARGET TR453 # 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 TR453.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 136.399 # # ============================================ # Comments from TR453.t06.bys.rdb # ============================================ # TARGET TR453 # 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 TR453.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 136.399 # # ============================================ # Comments from TR453.t06.alpha.rdb # ============================================ # TARGET TR453 # 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 TR453.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 136.399 # # ============================================ # Comments from TR453.t04.str2.rdb # ============================================ # TARGET TR453 # 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 TR453.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 130.223 # # ============================================ # Comments from TR453.t04.str4.rdb # ============================================ # TARGET TR453 # 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 TR453.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 130.223 # # ============================================ # Comments from TR453.t04.pb.rdb # ============================================ # TARGET TR453 # 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 TR453.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 130.223 # # ============================================ # Comments from TR453.t04.bys.rdb # ============================================ # TARGET TR453 # 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 TR453.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 130.223 # # ============================================ # Comments from TR453.t04.alpha.rdb # ============================================ # TARGET TR453 # 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 TR453.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 130.223 # # ============================================ # Comments from TR453.t2k.str2.rdb # ============================================ # TARGET TR453 # 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 TR453.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 91.1501 # # ============================================ # Comments from TR453.t2k.str4.rdb # ============================================ # TARGET TR453 # 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 TR453.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 91.1501 # # ============================================ # Comments from TR453.t2k.pb.rdb # ============================================ # TARGET TR453 # 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 TR453.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 91.1501 # # ============================================ # Comments from TR453.t2k.bys.rdb # ============================================ # TARGET TR453 # 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 TR453.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 91.1501 # # ============================================ # Comments from TR453.t2k.alpha.rdb # ============================================ # TARGET TR453 # 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 TR453.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 91.1501 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 D 0.1884 0.1969 0.6147 2 E 0.3833 0.1213 0.4954 3 I 0.6218 0.0642 0.3140 4 V 0.7038 0.0272 0.2690 5 Q 0.6611 0.0197 0.3192 6 R 0.4851 0.0536 0.4613 7 E 0.3533 0.1531 0.4936 8 D 0.1221 0.1546 0.7233 9 G 0.1226 0.0767 0.8007 10 S 0.4786 0.0218 0.4996 11 W 0.7052 0.0129 0.2819 12 L 0.7656 0.0119 0.2226 13 V 0.7503 0.0159 0.2339 14 D 0.6418 0.0314 0.3268 15 G 0.5229 0.0806 0.3965 16 M 0.4577 0.0938 0.4486 17 V 0.4857 0.0448 0.4695 18 S 0.2545 0.0358 0.7097 19 L 0.0246 0.7020 0.2734 20 D 0.0115 0.8528 0.1356 21 R 0.0110 0.8943 0.0947 22 F 0.0099 0.9034 0.0866 23 R 0.0094 0.9007 0.0899 24 E 0.0096 0.8881 0.1024 25 F 0.0219 0.7628 0.2153 26 F 0.0667 0.5111 0.4222 27 E 0.0887 0.2636 0.6477 28 L 0.1820 0.1759 0.6421 29 E 0.2249 0.1402 0.6348 30 A 0.2747 0.0621 0.6632 31 P 0.2030 0.0981 0.6988 32 L 0.2371 0.0608 0.7021 33 P 0.1768 0.1724 0.6508 34 G 0.1407 0.1731 0.6862 35 E 0.1702 0.2241 0.6057 36 A 0.1402 0.2124 0.6474 37 G 0.1047 0.1394 0.7559 38 G 0.1215 0.1208 0.7577 39 N 0.2480 0.1063 0.6457 40 I 0.3636 0.1617 0.4747 41 H 0.3594 0.2368 0.4039 42 T 0.3021 0.3757 0.3221 43 L 0.1030 0.6943 0.2027 44 A 0.0487 0.8045 0.1468 45 G 0.0484 0.8539 0.0977 46 V 0.0378 0.8841 0.0781 47 M 0.0404 0.8821 0.0775 48 L 0.0341 0.8800 0.0859 49 Y 0.0214 0.8813 0.0973 50 Q 0.0313 0.7743 0.1944 51 L 0.0692 0.4414 0.4893 52 G 0.0647 0.1793 0.7560 53 R 0.1818 0.1003 0.7179 54 V 0.2644 0.0281 0.7075 55 P 0.2634 0.0405 0.6961 56 S 0.2451 0.0973 0.6576 57 V 0.2380 0.1474 0.6146 58 T 0.2249 0.0951 0.6800 59 D 0.3992 0.0506 0.5501 60 R 0.7272 0.0146 0.2581 61 F 0.7580 0.0089 0.2331 62 E 0.7358 0.0091 0.2551 63 W 0.6634 0.0329 0.3037 64 N 0.4223 0.0572 0.5204 65 G 0.2058 0.0558 0.7384 66 F 0.5879 0.0142 0.3979 67 S 0.7160 0.0096 0.2744 68 F 0.7865 0.0060 0.2074 69 E 0.8026 0.0067 0.1908 70 V 0.7598 0.0050 0.2352 71 V 0.7439 0.0147 0.2415 72 D 0.6788 0.0161 0.3051 73 M 0.4104 0.1047 0.4850 74 D 0.2587 0.0930 0.6483 75 R 0.2217 0.1684 0.6098 76 T 0.3161 0.1340 0.5499 77 R 0.5548 0.0553 0.3899 78 V 0.5812 0.0434 0.3753 79 D 0.5323 0.0637 0.4040 80 K 0.7330 0.0209 0.2460 81 I 0.7381 0.0088 0.2531 82 L 0.7745 0.0074 0.2181 83 V 0.7622 0.0075 0.2303 84 Q 0.6083 0.0151 0.3765 85 R 0.4090 0.0866 0.5045 86 H 0.2513 0.1160 0.6327 87 H 0.2119 0.0848 0.7034