# This file is the result of combining several RDB files, specifically # T0564.t06.str2.rdb (weight 1.54425) # T0564.t06.str4.rdb (weight 0.924988) # T0564.t06.pb.rdb (weight 0.789901) # T0564.t06.bys.rdb (weight 0.748322) # T0564.t06.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 T0564.t06.str2.rdb # ============================================ # TARGET T0564 # 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 T0564.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 37.496 # # ============================================ # Comments from T0564.t06.str4.rdb # ============================================ # TARGET T0564 # 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 T0564.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 37.496 # # ============================================ # Comments from T0564.t06.pb.rdb # ============================================ # TARGET T0564 # 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 T0564.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 37.496 # # ============================================ # Comments from T0564.t06.bys.rdb # ============================================ # TARGET T0564 # 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 T0564.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 37.496 # # ============================================ # Comments from T0564.t06.alpha.rdb # ============================================ # TARGET T0564 # 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 T0564.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 37.496 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.1712 0.1174 0.7114 2 A 0.2563 0.0513 0.6924 3 P 0.2977 0.0648 0.6375 4 L 0.4036 0.0850 0.5114 5 Q 0.5446 0.0570 0.3985 6 Q 0.6597 0.0217 0.3186 7 K 0.7142 0.0204 0.2654 8 Q 0.7473 0.0109 0.2417 9 V 0.8033 0.0055 0.1912 10 V 0.7940 0.0063 0.1997 11 V 0.7452 0.0067 0.2482 12 S 0.6973 0.0314 0.2713 13 N 0.5850 0.0348 0.3802 14 K 0.4454 0.1085 0.4461 15 R 0.4578 0.0982 0.4440 16 E 0.4378 0.0609 0.5013 17 K 0.4331 0.0372 0.5297 18 P 0.3715 0.0657 0.5629 19 V 0.3134 0.1142 0.5724 20 N 0.2037 0.1824 0.6139 21 D 0.1747 0.1741 0.6511 22 R 0.1446 0.2840 0.5714 23 R 0.1674 0.2598 0.5728 24 S 0.1378 0.2671 0.5950 25 R 0.1145 0.2407 0.6447 26 Q 0.1509 0.2210 0.6281 27 Q 0.1728 0.2352 0.5920 28 E 0.2679 0.1624 0.5697 29 V 0.3801 0.0861 0.5338 30 S 0.3595 0.0425 0.5979 31 P 0.2837 0.0932 0.6231 32 A 0.2062 0.1292 0.6646 33 G 0.2050 0.0832 0.7118 34 T 0.3174 0.1042 0.5784 35 S 0.4972 0.0527 0.4501 36 M 0.6718 0.0304 0.2978 37 R 0.7781 0.0078 0.2141 38 Y 0.8226 0.0048 0.1726 39 E 0.8275 0.0042 0.1683 40 A 0.8299 0.0043 0.1658 41 S 0.8250 0.0049 0.1702 42 F 0.8032 0.0063 0.1906 43 K 0.7722 0.0080 0.2198 44 P 0.6591 0.0160 0.3249 45 L 0.5523 0.0665 0.3812 46 N 0.2903 0.0978 0.6119 47 G 0.1311 0.0854 0.7836 48 G 0.1635 0.0655 0.7710 49 L 0.4303 0.0531 0.5165 50 E 0.6297 0.0308 0.3396 51 K 0.7511 0.0177 0.2312 52 T 0.7861 0.0065 0.2073 53 F 0.8071 0.0066 0.1863 54 R 0.7956 0.0060 0.1984 55 L 0.7318 0.0110 0.2572 56 Q 0.4428 0.0294 0.5279 57 A 0.1855 0.4152 0.3993 58 Q 0.1661 0.4731 0.3608 59 Q 0.2194 0.4652 0.3155 60 Y 0.2137 0.4067 0.3796 61 H 0.2065 0.3400 0.4535 62 A 0.3153 0.2623 0.4224 63 L 0.3888 0.1649 0.4463 64 T 0.3543 0.0910 0.5546 65 V 0.2034 0.1898 0.6069 66 G 0.1262 0.1121 0.7617 67 D 0.2281 0.1265 0.6455 68 Q 0.3318 0.1109 0.5573 69 G 0.5301 0.0617 0.4082 70 T 0.7120 0.0229 0.2651 71 L 0.7585 0.0153 0.2262 72 S 0.7654 0.0211 0.2135 73 Y 0.7187 0.0184 0.2628 74 K 0.5702 0.0400 0.3898 75 G 0.4246 0.0512 0.5243 76 T 0.5477 0.0597 0.3927 77 R 0.6179 0.0796 0.3025 78 F 0.6528 0.0638 0.2834 79 V 0.6681 0.0527 0.2791 80 G 0.6631 0.0549 0.2820 81 F 0.6243 0.0577 0.3180 82 V 0.6160 0.0544 0.3296 83 S 0.4730 0.0870 0.4399 84 R 0.3046 0.0885 0.6069 85 T 0.2571 0.0414 0.7015 86 P 0.1626 0.1785 0.6590 87 D 0.1385 0.2063 0.6553 88 N 0.1459 0.1720 0.6820 89 E 0.1764 0.1828 0.6407