# This file is the result of combining several RDB files, specifically # T0555.t06.str2.rdb (weight 1.54425) # T0555.t06.str4.rdb (weight 0.924988) # T0555.t06.pb.rdb (weight 0.789901) # T0555.t06.bys.rdb (weight 0.748322) # T0555.t06.alpha.rdb (weight 0.678173) # T0555.t04.str2.rdb (weight 1.54425) # T0555.t04.str4.rdb (weight 0.924988) # T0555.t04.pb.rdb (weight 0.789901) # T0555.t04.bys.rdb (weight 0.748322) # T0555.t04.alpha.rdb (weight 0.678173) # T0555.t2k.str2.rdb (weight 1.54425) # T0555.t2k.str4.rdb (weight 0.924988) # T0555.t2k.pb.rdb (weight 0.789901) # T0555.t2k.bys.rdb (weight 0.748322) # T0555.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 T0555.t06.str2.rdb # ============================================ # TARGET T0555 # 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 T0555.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 27.539 # # ============================================ # Comments from T0555.t06.str4.rdb # ============================================ # TARGET T0555 # 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 T0555.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 27.539 # # ============================================ # Comments from T0555.t06.pb.rdb # ============================================ # TARGET T0555 # 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 T0555.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 27.539 # # ============================================ # Comments from T0555.t06.bys.rdb # ============================================ # TARGET T0555 # 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 T0555.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 27.539 # # ============================================ # Comments from T0555.t06.alpha.rdb # ============================================ # TARGET T0555 # 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 T0555.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 27.539 # # ============================================ # Comments from T0555.t04.str2.rdb # ============================================ # TARGET T0555 # 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 T0555.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 28.6782 # # ============================================ # Comments from T0555.t04.str4.rdb # ============================================ # TARGET T0555 # 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 T0555.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 28.6782 # # ============================================ # Comments from T0555.t04.pb.rdb # ============================================ # TARGET T0555 # 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 T0555.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 28.6782 # # ============================================ # Comments from T0555.t04.bys.rdb # ============================================ # TARGET T0555 # 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 T0555.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 28.6782 # # ============================================ # Comments from T0555.t04.alpha.rdb # ============================================ # TARGET T0555 # 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 T0555.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 28.6782 # # ============================================ # Comments from T0555.t2k.str2.rdb # ============================================ # TARGET T0555 # 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 T0555.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 25.4782 # # ============================================ # Comments from T0555.t2k.str4.rdb # ============================================ # TARGET T0555 # 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 T0555.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 25.4782 # # ============================================ # Comments from T0555.t2k.pb.rdb # ============================================ # TARGET T0555 # 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 T0555.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 25.4782 # # ============================================ # Comments from T0555.t2k.bys.rdb # ============================================ # TARGET T0555 # 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 T0555.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 25.4782 # # ============================================ # Comments from T0555.t2k.alpha.rdb # ============================================ # TARGET T0555 # 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 T0555.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 25.4782 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.2630 0.0381 0.6989 2 P 0.1810 0.1104 0.7087 3 Q 0.1951 0.2962 0.5087 4 S 0.2756 0.2914 0.4330 5 Y 0.3912 0.1814 0.4274 6 F 0.3725 0.1638 0.4637 7 N 0.2370 0.2143 0.5487 8 A 0.1307 0.4240 0.4454 9 A 0.1167 0.4585 0.4248 10 A 0.1321 0.3903 0.4776 11 K 0.2005 0.2646 0.5350 12 R 0.2484 0.2169 0.5347 13 Q 0.3284 0.1612 0.5104 14 K 0.3756 0.1749 0.4495 15 Y 0.4673 0.1335 0.3993 16 A 0.4895 0.1039 0.4066 17 M 0.4509 0.0843 0.4648 18 K 0.2783 0.0390 0.6827 19 P 0.1806 0.1446 0.6748 20 G 0.1145 0.1250 0.7606 21 L 0.1673 0.1468 0.6859 22 S 0.1599 0.1366 0.7035 23 A 0.0278 0.6387 0.3336 24 L 0.0181 0.7880 0.1939 25 E 0.0167 0.8556 0.1277 26 K 0.0097 0.8916 0.0987 27 N 0.0085 0.9138 0.0777 28 A 0.0083 0.9215 0.0701 29 V 0.0083 0.9230 0.0687 30 I 0.0083 0.9239 0.0678 31 K 0.0083 0.9225 0.0692 32 A 0.0084 0.9215 0.0702 33 A 0.0095 0.9152 0.0753 34 Y 0.0102 0.9081 0.0817 35 R 0.0118 0.9016 0.0866 36 Q 0.0247 0.8656 0.1097 37 I 0.0384 0.7953 0.1663 38 F 0.0467 0.6679 0.2853 39 E 0.0459 0.5652 0.3889 40 R 0.0530 0.4913 0.4557 41 D 0.0933 0.4233 0.4834 42 I 0.1626 0.3932 0.4442 43 T 0.2151 0.3549 0.4301 44 K 0.2013 0.4416 0.3571 45 A 0.1774 0.4741 0.3485 46 Y 0.1647 0.4597 0.3756 47 S 0.1288 0.4435 0.4276 48 Q 0.0881 0.4856 0.4263 49 S 0.1200 0.4559 0.4241 50 I 0.1334 0.5243 0.3423 51 S 0.1252 0.5690 0.3058 52 Y 0.1204 0.6456 0.2341 53 L 0.0690 0.7686 0.1624 54 E 0.0674 0.7844 0.1482 55 S 0.0855 0.7533 0.1611 56 Q 0.1101 0.6304 0.2595 57 V 0.1691 0.4961 0.3348 58 R 0.1664 0.3635 0.4701 59 N 0.0877 0.1665 0.7458 60 G 0.0551 0.1088 0.8361 61 D 0.2643 0.0670 0.6687 62 I 0.4191 0.0467 0.5341 63 S 0.2828 0.0732 0.6440 64 M 0.0823 0.6205 0.2972 65 K 0.0169 0.8460 0.1371 66 E 0.0104 0.9162 0.0734 67 F 0.0090 0.9191 0.0718 68 V 0.0087 0.9218 0.0694 69 R 0.0083 0.9213 0.0704 70 R 0.0086 0.9131 0.0783 71 L 0.0114 0.8661 0.1226 72 A 0.0215 0.7399 0.2386 73 K 0.0592 0.4900 0.4508 74 S 0.1298 0.3272 0.5430 75 P 0.0119 0.7246 0.2634 76 L 0.0112 0.8275 0.1613 77 Y 0.0173 0.8709 0.1119 78 R 0.0159 0.8785 0.1056 79 K 0.0204 0.8417 0.1378 80 Q 0.0330 0.7476 0.2194 81 F 0.0833 0.5433 0.3734 82 F 0.1386 0.3646 0.4968 83 E 0.1873 0.2219 0.5908 84 P 0.1229 0.3528 0.5243 85 F 0.1492 0.2493 0.6015 86 I 0.1364 0.2923 0.5713 87 N 0.1152 0.3441 0.5408 88 S 0.1054 0.5388 0.3558 89 R 0.0789 0.7071 0.2139 90 A 0.0761 0.8014 0.1225 91 L 0.0361 0.8742 0.0897 92 E 0.0239 0.8963 0.0797 93 L 0.0209 0.8988 0.0803 94 A 0.0165 0.8960 0.0876 95 F 0.0155 0.8855 0.0991 96 R 0.0156 0.8699 0.1145 97 H 0.0263 0.8272 0.1465 98 I 0.0530 0.6815 0.2655 99 L 0.0952 0.3459 0.5589 100 G 0.0951 0.1536 0.7513 101 R 0.1669 0.0849 0.7483 102 G 0.1850 0.0529 0.7621 103 P 0.1378 0.1638 0.6983 104 S 0.1222 0.1979 0.6799 105 S 0.1305 0.1939 0.6756 106 R 0.0137 0.7433 0.2430 107 E 0.0107 0.8560 0.1334 108 E 0.0104 0.9096 0.0799 109 V 0.0088 0.9172 0.0741 110 Q 0.0085 0.9153 0.0762 111 K 0.0085 0.9150 0.0766 112 Y 0.0101 0.9060 0.0840 113 F 0.0134 0.8995 0.0872 114 S 0.0135 0.9042 0.0823 115 I 0.0233 0.8793 0.0974 116 V 0.0359 0.8285 0.1357 117 S 0.0463 0.7096 0.2441 118 S 0.0516 0.4750 0.4734 119 G 0.0586 0.1713 0.7701 120 G 0.0642 0.1165 0.8192 121 L 0.1538 0.1275 0.7187 122 P 0.0900 0.5578 0.3521 123 A 0.1105 0.6831 0.2064 124 L 0.0778 0.7722 0.1500 125 V 0.0595 0.8123 0.1281 126 D 0.0496 0.8179 0.1325 127 A 0.0503 0.7756 0.1741 128 L 0.0844 0.5982 0.3174 129 V 0.1323 0.4305 0.4372 130 D 0.1226 0.2612 0.6161 131 S 0.0982 0.3833 0.5185 132 Q 0.0123 0.7544 0.2333 133 E 0.0103 0.8535 0.1362 134 Y 0.0123 0.8909 0.0968 135 A 0.0112 0.8856 0.1032 136 D 0.0130 0.8409 0.1461 137 Y 0.0257 0.6708 0.3034 138 F 0.0715 0.2618 0.6666 139 G 0.0750 0.1756 0.7493 140 E 0.1102 0.2649 0.6249 141 E 0.1831 0.2007 0.6162 142 T 0.3505 0.1133 0.5362 143 V 0.4241 0.0544 0.5216 144 P 0.4702 0.0805 0.4493 145 Y 0.4900 0.1058 0.4042 146 L 0.4174 0.1083 0.4743 147 R 0.2759 0.1089 0.6152 148 G 0.1455 0.0890 0.7655