# This file is the result of combining several RDB files, specifically # T0399.t2k.str2.rdb (weight 1.54425) # T0399.t2k.str4.rdb (weight 0.924988) # T0399.t2k.pb.rdb (weight 0.789901) # T0399.t2k.bys.rdb (weight 0.748322) # T0399.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 T0399.t2k.str2.rdb # ============================================ # TARGET T0399 # 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 T0399.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 23 # # ============================================ # Comments from T0399.t2k.str4.rdb # ============================================ # TARGET T0399 # 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 T0399.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 23 # # ============================================ # Comments from T0399.t2k.pb.rdb # ============================================ # TARGET T0399 # 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 T0399.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 23 # # ============================================ # Comments from T0399.t2k.bys.rdb # ============================================ # TARGET T0399 # 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 T0399.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 23 # # ============================================ # Comments from T0399.t2k.alpha.rdb # ============================================ # TARGET T0399 # 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 T0399.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 23 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 V 0.4369 0.0643 0.4988 2 T 0.3406 0.0619 0.5974 3 T 0.3128 0.1834 0.5038 4 D 0.2894 0.2212 0.4894 5 Q 0.3109 0.2290 0.4602 6 N 0.3082 0.1840 0.5078 7 H 0.3767 0.1370 0.4863 8 F 0.3881 0.1132 0.4987 9 S 0.2950 0.1294 0.5756 10 G 0.1961 0.1341 0.6699 11 G 0.1528 0.1353 0.7120 12 T 0.2017 0.1530 0.6454 13 S 0.1714 0.1134 0.7153 14 I 0.0123 0.7631 0.2245 15 E 0.0102 0.8628 0.1269 16 Q 0.0104 0.9132 0.0765 17 L 0.0091 0.9150 0.0759 18 K 0.0096 0.9107 0.0798 19 Q 0.0108 0.8880 0.1012 20 W 0.0238 0.7504 0.2258 21 F 0.0591 0.3244 0.6164 22 G 0.0573 0.1012 0.8415 23 D 0.1648 0.0309 0.8042 24 P 0.1298 0.2712 0.5990 25 N 0.1155 0.2729 0.6117 26 K 0.1651 0.2548 0.5801 27 S 0.1940 0.1753 0.6307 28 E 0.2333 0.2112 0.5556 29 Q 0.2945 0.1999 0.5057 30 R 0.3205 0.1894 0.4901 31 N 0.2963 0.2044 0.4993 32 A 0.2195 0.1750 0.6055 33 G 0.1362 0.1338 0.7300 34 N 0.2743 0.0738 0.6519 35 I 0.5392 0.0225 0.4383 36 T 0.6523 0.0200 0.3277 37 L 0.6819 0.0303 0.2878 38 D 0.6370 0.0497 0.3133 39 S 0.7262 0.0321 0.2417 40 Y 0.7325 0.0241 0.2435 41 T 0.7424 0.0222 0.2354 42 W 0.6774 0.0368 0.2858 43 V 0.5227 0.0603 0.4171 44 K 0.3526 0.1060 0.5414 45 D 0.1735 0.0971 0.7294 46 G 0.2083 0.0749 0.7168 47 A 0.5527 0.0239 0.4234 48 V 0.7222 0.0122 0.2657 49 I 0.7884 0.0094 0.2021 50 N 0.8033 0.0059 0.1908 51 A 0.8111 0.0066 0.1823 52 Q 0.7997 0.0076 0.1926 53 L 0.7313 0.0185 0.2502 54 Y 0.5226 0.0558 0.4216 55 K 0.2378 0.0882 0.6740 56 N 0.1438 0.1064 0.7498 57 S 0.2254 0.1603 0.6144 58 T 0.4994 0.1324 0.3681 59 V 0.6327 0.1191 0.2481 60 A 0.6338 0.1487 0.2176 61 R 0.5961 0.1869 0.2170 62 S 0.4987 0.2377 0.2636 63 I 0.4177 0.2784 0.3039 64 S 0.2366 0.2549 0.5084 65 N 0.1761 0.1662 0.6576 66 F 0.3504 0.1135 0.5361 67 S 0.4401 0.1077 0.4522 68 F 0.4306 0.1413 0.4281 69 S 0.2924 0.1929 0.5146 70 R 0.1759 0.3796 0.4445 71 E 0.1304 0.4345 0.4352 72 A 0.1294 0.4075 0.4631 73 K 0.1766 0.2417 0.5817 74 I 0.2654 0.1321 0.6025 75 G 0.1758 0.0562 0.7680 76 K 0.0407 0.6249 0.3344 77 E 0.0233 0.7613 0.2154 78 D 0.0488 0.7113 0.2399 79 Y 0.0421 0.7714 0.1866 80 D 0.0265 0.8117 0.1618 81 E 0.0467 0.7204 0.2329 82 L 0.0927 0.6700 0.2373 83 K 0.1222 0.5121 0.3657 84 I 0.1128 0.2763 0.6109 85 G 0.0649 0.1582 0.7769 86 E 0.1149 0.2519 0.6332 87 S 0.1312 0.2483 0.6205 88 Y 0.0264 0.7373 0.2363 89 K 0.0116 0.8608 0.1275 90 K 0.0124 0.9023 0.0853 91 V 0.0126 0.9077 0.0797 92 V 0.0112 0.9069 0.0819 93 E 0.0105 0.8995 0.0899 94 K 0.0257 0.7589 0.2154 95 L 0.0609 0.3679 0.5712 96 G 0.0563 0.0957 0.8480 97 E 0.1692 0.0441 0.7867 98 P 0.1633 0.1984 0.6383 99 D 0.1412 0.2572 0.6016 100 V 0.2320 0.2709 0.4971 101 L 0.3039 0.2426 0.4535 102 S 0.3169 0.2390 0.4441 103 Q 0.2694 0.3466 0.3840 104 S 0.2338 0.3313 0.4349 105 M 0.2270 0.2817 0.4913 106 S 0.2301 0.2201 0.5498 107 S 0.1730 0.1778 0.6492 108 D 0.1540 0.1589 0.6872 109 K 0.1207 0.3574 0.5219 110 E 0.1532 0.4116 0.4352 111 E 0.2847 0.3456 0.3698 112 M 0.3814 0.3327 0.2860 113 Q 0.4754 0.3076 0.2169 114 T 0.5452 0.2575 0.1974 115 V 0.5180 0.2835 0.1985 116 W 0.4143 0.3404 0.2453 117 S 0.3321 0.3503 0.3176 118 S 0.1962 0.2177 0.5861 119 G 0.1587 0.1040 0.7373 120 I 0.3271 0.1040 0.5689 121 K 0.3616 0.1081 0.5303 122 T 0.3012 0.1201 0.5787 123 K 0.1888 0.1171 0.6941 124 S 0.1989 0.1137 0.6875 125 S 0.1429 0.1993 0.6578 126 S 0.2230 0.1182 0.6588 127 A 0.3523 0.0672 0.5804 128 T 0.5950 0.0263 0.3788 129 I 0.7472 0.0077 0.2451 130 E 0.8055 0.0049 0.1896 131 L 0.8177 0.0047 0.1776 132 Y 0.8075 0.0050 0.1876 133 F 0.6958 0.0084 0.2958 134 E 0.4967 0.0583 0.4451 135 N 0.2269 0.0630 0.7101 136 G 0.1440 0.0825 0.7736 137 L 0.4587 0.0463 0.4949 138 L 0.6245 0.0393 0.3362 139 K 0.6020 0.0742 0.3238 140 N 0.5285 0.1302 0.3413 141 K 0.2757 0.3339 0.3904 142 T 0.2277 0.3413 0.4310 143 Q 0.1882 0.3597 0.4521 144 K 0.1544 0.2903 0.5553 145 D 0.1520 0.1800 0.6679 146 L 0.1969 0.2449 0.5582 147 E 0.2352 0.2295 0.5354