# This file is the result of combining several RDB files, specifically # T0321.t06.dssp-ebghstl.rdb (weight 1.53986) # T0321.t06.stride-ebghtl.rdb (weight 1.24869) # T0321.t06.str2.rdb (weight 1.54758) # T0321.t06.alpha.rdb (weight 0.659012) # T0321.t04.dssp-ebghstl.rdb (weight 1.53986) # T0321.t04.stride-ebghtl.rdb (weight 1.24869) # T0321.t04.str2.rdb (weight 1.54758) # T0321.t04.alpha.rdb (weight 0.659012) # T0321.t2k.dssp-ebghstl.rdb (weight 1.53986) # T0321.t2k.stride-ebghtl.rdb (weight 1.24869) # T0321.t2k.str2.rdb (weight 1.54758) # T0321.t2k.alpha.rdb (weight 0.659012) # 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 T0321.t06.dssp-ebghstl.rdb # ============================================ # TARGET T0321 # Using neural net t04-2621-IDGaaH13-3-13-7-13-9-13-11-ebghstl-dssp-seeded.net # This is a 4-layer network, with # window units # 3 13 # 7 13 # 9 13 # 11 7 (1 EBGHSTL ) # The input amino acid frequencies were determined from # alignment T0321.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 49 # # ============================================ # Comments from T0321.t06.stride-ebghtl.rdb # ============================================ # TARGET T0321 # Using neural net t04-2621-IDGaaH13-3-13-7-13-9-13-11-ebghtl-stride-seeded.net # This is a 4-layer network, with # window units # 3 13 # 7 13 # 9 13 # 11 6 (1 EBGHTL ) # The input amino acid frequencies were determined from # alignment T0321.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 49 # # ============================================ # Comments from T0321.t06.str2.rdb # ============================================ # TARGET T0321 # Using neural net dunbrack-30pc-1763-t2k-thin90-IDGaaH13-3-13-7-13-9-13-11-t1c2-str2-from-empty.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 T0321.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 49 # # ============================================ # Comments from T0321.t06.alpha.rdb # ============================================ # TARGET T0321 # Using neural net t04-2621-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 T0321.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 49 # # ============================================ # Comments from T0321.t04.dssp-ebghstl.rdb # ============================================ # TARGET T0321 # Using neural net t04-2621-IDGaaH13-3-13-7-13-9-13-11-ebghstl-dssp-seeded.net # This is a 4-layer network, with # window units # 3 13 # 7 13 # 9 13 # 11 7 (1 EBGHSTL ) # The input amino acid frequencies were determined from # alignment T0321.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 49.5759 # # ============================================ # Comments from T0321.t04.stride-ebghtl.rdb # ============================================ # TARGET T0321 # Using neural net t04-2621-IDGaaH13-3-13-7-13-9-13-11-ebghtl-stride-seeded.net # This is a 4-layer network, with # window units # 3 13 # 7 13 # 9 13 # 11 6 (1 EBGHTL ) # The input amino acid frequencies were determined from # alignment T0321.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 49.5759 # # ============================================ # Comments from T0321.t04.str2.rdb # ============================================ # TARGET T0321 # Using neural net dunbrack-30pc-1763-t2k-thin90-IDGaaH13-3-13-7-13-9-13-11-t1c2-str2-from-empty.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 T0321.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 49.5759 # # ============================================ # Comments from T0321.t04.alpha.rdb # ============================================ # TARGET T0321 # Using neural net t04-2621-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 T0321.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 49.5759 # # ============================================ # Comments from T0321.t2k.dssp-ebghstl.rdb # ============================================ # TARGET T0321 # Using neural net t2k-5740-IDaaHr-5-15-7-15-9-15-13-ebghstl-seeded.net # This is a 4-layer network, with # window units # 5 15 # 7 15 # 9 15 # 13 7 (1 EBGHSTL ) # The input amino acid frequencies were determined from # alignment T0321.t2k-thin90.a2m.gz # with weighted counts, using HenikoffWeight(-1 bits/column, 1) # Counts were regularized to probabilities using # /projects/compbio/lib/recode3.20comp # Total sequence weight for alignment was 37 # # ============================================ # Comments from T0321.t2k.stride-ebghtl.rdb # ============================================ # TARGET T0321 # Using neural net t2k-5651-IDaaHr-5-15-7-15-9-15-13-ebghtl-seeded.net # This is a 4-layer network, with # window units # 5 15 # 7 15 # 9 15 # 13 6 (1 EBGHTL ) # The input amino acid frequencies were determined from # alignment T0321.t2k-thin90.a2m.gz # with weighted counts, using HenikoffWeight(-1 bits/column, 1) # Counts were regularized to probabilities using # /projects/compbio/lib/recode3.20comp # Total sequence weight for alignment was 37 # # ============================================ # Comments from T0321.t2k.str2.rdb # ============================================ # TARGET T0321 # Using neural net dunbrack-30pc-1763-t2k-thin90-IDGaaH13-3-13-7-13-9-13-11-t1c2-str2-from-empty.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 T0321.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 31.7373 # # ============================================ # Comments from T0321.t2k.alpha.rdb # ============================================ # TARGET T0321 # Using neural net t2k-5651-IDaaHr-5-15-7-15-9-15-13-alpha-seeded.net # This is a 4-layer network, with # window units # 5 15 # 7 15 # 9 15 # 13 11 (1 ABCDEFGHIST ) # The input amino acid frequencies were determined from # alignment T0321.t2k-thin90.a2m.gz # with weighted counts, using HenikoffWeight(-1 bits/column, 1) # Counts were regularized to probabilities using # /projects/compbio/lib/recode3.20comp # Total sequence weight for alignment was 37 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 V 0.2082 0.0641 0.7276 2 E 0.2744 0.0793 0.6462 3 D 0.2441 0.1180 0.6379 4 R 0.1511 0.1324 0.7164 5 M 0.1021 0.1291 0.7688 6 N 0.0539 0.2181 0.7280 7 D 0.0522 0.2687 0.6791 8 P 0.0415 0.5743 0.3841 9 F 0.0729 0.6262 0.3009 10 I 0.0957 0.6535 0.2507 11 M 0.1595 0.6136 0.2269 12 S 0.2455 0.4829 0.2717 13 Q 0.2172 0.4634 0.3194 14 N 0.2644 0.3544 0.3812 15 E 0.2042 0.2943 0.5015 16 V 0.1189 0.1372 0.7439 17 K 0.0321 0.0990 0.8689 18 G 0.0329 0.0477 0.9194 19 K 0.2073 0.0173 0.7754 20 K 0.6422 0.0053 0.3525 21 V 0.9075 0.0043 0.0881 22 G 0.9257 0.0038 0.0705 23 V 0.9262 0.0034 0.0704 24 V 0.8714 0.0183 0.1103 25 G 0.6896 0.0185 0.2918 26 H 0.3634 0.0333 0.6033 27 F 0.1357 0.0468 0.8175 28 P 0.0511 0.3035 0.6453 29 H 0.0532 0.4394 0.5074 30 L 0.0303 0.7220 0.2477 31 E 0.0227 0.7684 0.2090 32 S 0.0140 0.7765 0.2095 33 L 0.0155 0.7403 0.2442 34 L 0.0277 0.6822 0.2901 35 E 0.0226 0.6733 0.3041 36 P 0.0276 0.5893 0.3832 37 I 0.0639 0.4077 0.5283 38 C 0.1172 0.1269 0.7558 39 D 0.1933 0.0781 0.7286 40 L 0.5629 0.0376 0.3995 41 S 0.7885 0.0189 0.1925 42 I 0.8854 0.0103 0.1043 43 L 0.8714 0.0131 0.1156 44 E 0.7866 0.0260 0.1874 45 W 0.5911 0.0331 0.3757 46 S 0.2193 0.0243 0.7564 47 P 0.1046 0.0472 0.8482 48 E 0.0674 0.0687 0.8640 49 E 0.0491 0.1481 0.8028 50 G 0.0453 0.1080 0.8467 51 D 0.0904 0.0932 0.8164 52 Y 0.1470 0.0362 0.8168 53 P 0.0775 0.0456 0.8769 54 L 0.0099 0.6867 0.3035 55 P 0.0065 0.7759 0.2176 56 A 0.0079 0.8197 0.1724 57 S 0.0113 0.8151 0.1736 58 E 0.0086 0.7212 0.2701 59 F 0.0107 0.6092 0.3801 60 I 0.0286 0.5631 0.4083 61 L 0.0314 0.3841 0.5845 62 P 0.0168 0.3891 0.5942 63 E 0.0296 0.3219 0.6485 64 C 0.1182 0.0642 0.8176 65 D 0.1737 0.0962 0.7301 66 Y 0.9062 0.0092 0.0846 67 V 0.9306 0.0053 0.0641 68 Y 0.9271 0.0078 0.0651 69 I 0.8893 0.0194 0.0913 70 T 0.5609 0.0538 0.3853 71 C 0.1835 0.3701 0.4465 72 A 0.0824 0.6274 0.2902 73 S 0.0655 0.7476 0.1869 74 V 0.0845 0.7439 0.1716 75 V 0.0749 0.6900 0.2352 76 D 0.0410 0.6207 0.3383 77 K 0.0213 0.6161 0.3626 78 T 0.0339 0.7180 0.2481 79 L 0.0052 0.9406 0.0542 80 P 0.0048 0.9547 0.0405 81 R 0.0048 0.9534 0.0419 82 L 0.0048 0.9478 0.0474 83 L 0.0050 0.9233 0.0716 84 E 0.0051 0.8183 0.1765 85 L 0.0087 0.6707 0.3206 86 S 0.0697 0.3523 0.5780 87 R 0.0265 0.3310 0.6425 88 N 0.0445 0.2378 0.7177 89 A 0.1354 0.1659 0.6987 90 R 0.4378 0.0827 0.4796 91 R 0.8227 0.0161 0.1612 92 I 0.9152 0.0113 0.0735 93 T 0.9236 0.0051 0.0713 94 L 0.9161 0.0049 0.0790 95 V 0.7715 0.0283 0.2002 96 G 0.2844 0.0237 0.6920 97 P 0.1208 0.0424 0.8367 98 G 0.0929 0.0666 0.8405 99 T 0.0891 0.0768 0.8341 100 P 0.1335 0.0978 0.7687 101 L 0.1613 0.1573 0.6815 102 A 0.1364 0.1427 0.7209 103 P 0.0784 0.5400 0.3816 104 V 0.0800 0.5985 0.3215 105 L 0.0763 0.6448 0.2789 106 F 0.0619 0.5602 0.3779 107 E 0.0540 0.3939 0.5521 108 H 0.0671 0.1586 0.7743 109 G 0.0777 0.0430 0.8793 110 L 0.2603 0.0261 0.7137 111 Q 0.5943 0.0405 0.3652 112 E 0.8344 0.0227 0.1429 113 L 0.8576 0.0163 0.1261 114 S 0.7970 0.0175 0.1855 115 G 0.7902 0.0147 0.1951 116 F 0.8079 0.0098 0.1823 117 M 0.7967 0.0104 0.1928 118 V 0.6085 0.0169 0.3746 119 K 0.3029 0.0378 0.6593 120 D 0.1339 0.0185 0.8476 121 N 0.0053 0.9044 0.0903 122 A 0.0049 0.9433 0.0518 123 R 0.0049 0.9530 0.0422 124 A 0.0047 0.9575 0.0378 125 F 0.0047 0.9562 0.0390 126 R 0.0051 0.9567 0.0382 127 I 0.0048 0.9563 0.0388 128 V 0.0055 0.9495 0.0450 129 A 0.0060 0.9050 0.0890 130 G 0.0195 0.6502 0.3303 131 A 0.0310 0.3595 0.6095 132 E 0.0551 0.1829 0.7620 133 K 0.0986 0.1579 0.7435 134 V 0.2521 0.1931 0.5548 135 K 0.4684 0.1887 0.3429 136 I 0.5079 0.1855 0.3065 137 Y 0.4278 0.1515 0.4208 138 S 0.3111 0.1447 0.5442 139 A 0.1344 0.1678 0.6978 140 G 0.2016 0.1220 0.6764 141 Q 0.4934 0.0645 0.4420 142 K 0.7194 0.0403 0.2403 143 V 0.8191 0.0253 0.1556 144 T 0.8418 0.0184 0.1398 145 I 0.7629 0.0199 0.2173 146 K 0.5381 0.0332 0.4287 147 K 0.2016 0.0321 0.7663