# This file is the result of combining several RDB files, specifically # T0429.t06.str2.rdb (weight 1.54425) # T0429.t06.str4.rdb (weight 0.924988) # T0429.t06.pb.rdb (weight 0.789901) # T0429.t06.bys.rdb (weight 0.748322) # T0429.t06.alpha.rdb (weight 0.678173) # T0429.t04.str2.rdb (weight 1.54425) # T0429.t04.str4.rdb (weight 0.924988) # T0429.t04.pb.rdb (weight 0.789901) # T0429.t04.bys.rdb (weight 0.748322) # T0429.t04.alpha.rdb (weight 0.678173) # T0429.t2k.str2.rdb (weight 1.54425) # T0429.t2k.str4.rdb (weight 0.924988) # T0429.t2k.pb.rdb (weight 0.789901) # T0429.t2k.bys.rdb (weight 0.748322) # T0429.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 T0429.t06.str2.rdb # ============================================ # TARGET T0429 # 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 T0429.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 14.1464 # # ============================================ # Comments from T0429.t06.str4.rdb # ============================================ # TARGET T0429 # 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 T0429.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 14.1464 # # ============================================ # Comments from T0429.t06.pb.rdb # ============================================ # TARGET T0429 # 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 T0429.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 14.1464 # # ============================================ # Comments from T0429.t06.bys.rdb # ============================================ # TARGET T0429 # 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 T0429.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 14.1464 # # ============================================ # Comments from T0429.t06.alpha.rdb # ============================================ # TARGET T0429 # 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 T0429.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 14.1464 # # ============================================ # Comments from T0429.t04.str2.rdb # ============================================ # TARGET T0429 # 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 T0429.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 13.0679 # # ============================================ # Comments from T0429.t04.str4.rdb # ============================================ # TARGET T0429 # 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 T0429.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 13.0679 # # ============================================ # Comments from T0429.t04.pb.rdb # ============================================ # TARGET T0429 # 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 T0429.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 13.0679 # # ============================================ # Comments from T0429.t04.bys.rdb # ============================================ # TARGET T0429 # 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 T0429.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 13.0679 # # ============================================ # Comments from T0429.t04.alpha.rdb # ============================================ # TARGET T0429 # 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 T0429.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 13.0679 # # ============================================ # Comments from T0429.t2k.str2.rdb # ============================================ # TARGET T0429 # 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 T0429.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 7.43204 # # ============================================ # Comments from T0429.t2k.str4.rdb # ============================================ # TARGET T0429 # 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 T0429.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 7.43204 # # ============================================ # Comments from T0429.t2k.pb.rdb # ============================================ # TARGET T0429 # 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 T0429.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 7.43204 # # ============================================ # Comments from T0429.t2k.bys.rdb # ============================================ # TARGET T0429 # 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 T0429.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 7.43204 # # ============================================ # Comments from T0429.t2k.alpha.rdb # ============================================ # TARGET T0429 # 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 T0429.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 7.43204 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 R 0.2891 0.1554 0.5555 2 T 0.2335 0.1306 0.6359 3 A 0.1140 0.4894 0.3965 4 R 0.1227 0.5733 0.3040 5 E 0.3194 0.3786 0.3021 6 L 0.4915 0.2204 0.2881 7 Y 0.6007 0.1265 0.2728 8 A 0.6572 0.0868 0.2560 9 N 0.7013 0.0548 0.2439 10 V 0.7458 0.0326 0.2216 11 V 0.6945 0.0325 0.2730 12 L 0.5831 0.0481 0.3689 13 G 0.2475 0.0580 0.6946 14 D 0.1597 0.1441 0.6962 15 D 0.1220 0.2309 0.6471 16 S 0.1660 0.2082 0.6258 17 L 0.1822 0.2363 0.5815 18 N 0.1492 0.2454 0.6054 19 D 0.1469 0.1661 0.6870 20 C 0.3646 0.0915 0.5438 21 R 0.5764 0.0498 0.3738 22 I 0.6860 0.0359 0.2781 23 I 0.6957 0.0376 0.2666 24 F 0.5899 0.0591 0.3510 25 V 0.3477 0.2890 0.3633 26 D 0.3021 0.3578 0.3401 27 E 0.3371 0.3586 0.3043 28 V 0.4685 0.2621 0.2694 29 F 0.5757 0.1718 0.2525 30 K 0.6153 0.1246 0.2601 31 I 0.5693 0.1024 0.3283 32 E 0.4328 0.1013 0.4659 33 R 0.3076 0.0519 0.6405 34 P 0.1672 0.1406 0.6922 35 G 0.1066 0.1204 0.7730 36 E 0.2037 0.1518 0.6445 37 R 0.2444 0.1569 0.5987 38 E 0.2158 0.2761 0.5082 39 N 0.2410 0.2860 0.4730 40 L 0.2336 0.3600 0.4064 41 Y 0.2184 0.3434 0.4382 42 F 0.1934 0.3053 0.5014 43 Q 0.1382 0.1787 0.6831 44 G 0.1019 0.1424 0.7557 45 M 0.1967 0.1244 0.6789 46 W 0.2512 0.1649 0.5838 47 D 0.2073 0.2052 0.5875 48 E 0.1293 0.3709 0.4998 49 T 0.1423 0.2305 0.6272 50 E 0.1907 0.1619 0.6473 51 L 0.1653 0.2697 0.5649 52 G 0.1927 0.2347 0.5725 53 L 0.2468 0.3517 0.4015 54 Y 0.2450 0.4040 0.3510 55 K 0.2583 0.3825 0.3593 56 V 0.2169 0.3510 0.4321 57 N 0.1323 0.3944 0.4733 58 E 0.1060 0.4083 0.4857 59 Y 0.1349 0.2763 0.5888 60 V 0.0813 0.4545 0.4642 61 D 0.0967 0.3762 0.5271 62 A 0.0830 0.4847 0.4323 63 R 0.1096 0.3767 0.5137 64 D 0.1716 0.2889 0.5395 65 T 0.1272 0.3748 0.4979 66 N 0.1914 0.3031 0.5056 67 M 0.2747 0.2285 0.4968 68 G 0.3614 0.1927 0.4459 69 A 0.5014 0.1463 0.3523 70 W 0.5550 0.1161 0.3290 71 F 0.5230 0.1279 0.3491 72 E 0.4436 0.1385 0.4179 73 A 0.4064 0.1370 0.4566 74 Q 0.5263 0.0953 0.3784 75 V 0.6608 0.0597 0.2796 76 V 0.6960 0.0419 0.2621 77 R 0.7129 0.0281 0.2590 78 V 0.6563 0.0458 0.2979 79 T 0.4974 0.0533 0.4493 80 R 0.3113 0.0920 0.5967