# This file is the result of combining several RDB files, specifically # T0304.t2k.dssp-ebghstl.rdb (weight 1.53986) # T0304.t2k.stride-ebghtl.rdb (weight 1.24869) # T0304.t2k.str2.rdb (weight 1.54758) # T0304.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 T0304.t2k.dssp-ebghstl.rdb # ============================================ # TARGET T0304 # 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 T0304.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 28 # # ============================================ # Comments from T0304.t2k.stride-ebghtl.rdb # ============================================ # TARGET T0304 # 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 T0304.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 28 # # ============================================ # Comments from T0304.t2k.str2.rdb # ============================================ # TARGET T0304 # 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 T0304.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 4.49623 # # ============================================ # Comments from T0304.t2k.alpha.rdb # ============================================ # TARGET T0304 # 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 T0304.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 28 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.0898 0.0814 0.8287 2 S 0.1405 0.1425 0.7169 3 D 0.1138 0.1975 0.6888 4 T 0.1415 0.1452 0.7133 5 L 0.1312 0.0730 0.7958 6 P 0.0760 0.0926 0.8314 7 G 0.0932 0.0755 0.8312 8 T 0.1485 0.0511 0.8004 9 T 0.1318 0.0301 0.8381 10 L 0.1031 0.0343 0.8626 11 P 0.0664 0.1217 0.8118 12 D 0.0519 0.2244 0.7238 13 D 0.0574 0.2084 0.7342 14 N 0.0665 0.1392 0.7943 15 H 0.0695 0.1055 0.8250 16 D 0.1029 0.0760 0.8211 17 R 0.1324 0.0478 0.8199 18 P 0.1396 0.0887 0.7717 19 W 0.1606 0.1502 0.6892 20 W 0.1876 0.1368 0.6755 21 G 0.1371 0.0822 0.7807 22 L 0.1760 0.0446 0.7794 23 P 0.1727 0.0391 0.7882 24 C 0.2720 0.0520 0.6760 25 T 0.3515 0.0434 0.6052 26 V 0.3791 0.0333 0.5876 27 T 0.2207 0.0364 0.7430 28 P 0.1301 0.1747 0.6952 29 C 0.1291 0.2143 0.6566 30 F 0.1632 0.2215 0.6153 31 G 0.2006 0.1521 0.6473 32 A 0.3688 0.1648 0.4663 33 R 0.6020 0.2018 0.1962 34 L 0.6558 0.1864 0.1578 35 V 0.6569 0.1630 0.1801 36 Q 0.5431 0.1634 0.2935 37 E 0.2225 0.2151 0.5624 38 G 0.0623 0.2948 0.6429 39 N 0.0955 0.3968 0.5077 40 R 0.1170 0.6389 0.2440 41 L 0.1047 0.7445 0.1508 42 H 0.0915 0.7233 0.1851 43 Y 0.1089 0.7410 0.1502 44 L 0.0593 0.7554 0.1853 45 A 0.0606 0.6699 0.2694 46 D 0.0334 0.5951 0.3715 47 R 0.0447 0.4751 0.4802 48 A 0.1142 0.1872 0.6987 49 G 0.1895 0.0447 0.7657 50 I 0.5023 0.0388 0.4589 51 R 0.6252 0.0454 0.3295 52 G 0.7059 0.0212 0.2729 53 L 0.5064 0.0205 0.4731 54 F 0.1839 0.0163 0.7998 55 S 0.0722 0.0157 0.9121 56 D 0.0134 0.6897 0.2969 57 A 0.0056 0.8678 0.1265 58 D 0.0067 0.8716 0.1217 59 A 0.0179 0.8307 0.1514 60 Y 0.0236 0.6748 0.3016 61 H 0.0349 0.6591 0.3060 62 L 0.0111 0.8410 0.1479 63 D 0.0067 0.8912 0.1022 64 Q 0.0067 0.8846 0.1088 65 A 0.0108 0.8855 0.1037 66 F 0.0075 0.9328 0.0597 67 P 0.0048 0.9573 0.0379 68 L 0.0048 0.9572 0.0379 69 L 0.0048 0.9555 0.0396 70 M 0.0049 0.9580 0.0371 71 K 0.0051 0.9512 0.0437 72 Q 0.0050 0.9488 0.0462 73 L 0.0050 0.9471 0.0480 74 E 0.0057 0.9401 0.0542 75 L 0.0060 0.9366 0.0574 76 M 0.0111 0.9202 0.0687 77 L 0.0338 0.8312 0.1350 78 T 0.0406 0.6551 0.3043 79 S 0.0591 0.3675 0.5734 80 G 0.0446 0.0896 0.8658 81 E 0.1442 0.0549 0.8009 82 L 0.2080 0.0343 0.7577 83 N 0.1016 0.0263 0.8722 84 P 0.0218 0.3302 0.6480 85 R 0.0371 0.3049 0.6580 86 H 0.1484 0.2640 0.5876 87 Q 0.3486 0.0888 0.5626 88 H 0.5582 0.0413 0.4005 89 T 0.7515 0.0202 0.2282 90 V 0.8328 0.0113 0.1559 91 T 0.8811 0.0075 0.1115 92 L 0.8836 0.0091 0.1073 93 Y 0.8572 0.0133 0.1295 94 A 0.7297 0.0275 0.2428 95 K 0.1800 0.0607 0.7593 96 G 0.1685 0.0454 0.7861 97 L 0.6423 0.0309 0.3268 98 T 0.7397 0.0228 0.2375 99 C 0.7108 0.0468 0.2424 100 K 0.6161 0.0824 0.3015 101 A 0.4001 0.1457 0.4542 102 D 0.3315 0.1340 0.5346 103 T 0.2091 0.1214 0.6695 104 L 0.1698 0.0687 0.7614 105 S 0.1675 0.0632 0.7693 106 S 0.2706 0.0520 0.6774 107 C 0.3685 0.0313 0.6003 108 D 0.5285 0.0271 0.4444 109 Y 0.8724 0.0099 0.1177 110 V 0.9194 0.0042 0.0764 111 Y 0.9223 0.0045 0.0732 112 L 0.9194 0.0039 0.0767 113 A 0.8823 0.0072 0.1105 114 V 0.8052 0.0150 0.1799 115 Y 0.5899 0.0101 0.4000 116 P 0.3237 0.0390 0.6373 117 T 0.1641 0.0382 0.7976 118 P 0.0555 0.1982 0.7463 119 E 0.0492 0.1722 0.7786 120 M 0.1011 0.1159 0.7830 121 K 0.0758 0.0803 0.8439 122 N 0.0571 0.0405 0.9024