# This file is the result of combining several RDB files, specifically # T0399.t06.str2.rdb (weight 1.54425) # T0399.t06.str4.rdb (weight 0.924988) # T0399.t06.pb.rdb (weight 0.789901) # T0399.t06.bys.rdb (weight 0.748322) # T0399.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 T0399.t06.str2.rdb # ============================================ # TARGET T0399 # 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 T0399.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 78 # # ============================================ # Comments from T0399.t06.str4.rdb # ============================================ # TARGET T0399 # 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 T0399.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 78 # # ============================================ # Comments from T0399.t06.pb.rdb # ============================================ # TARGET T0399 # 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 T0399.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 78 # # ============================================ # Comments from T0399.t06.bys.rdb # ============================================ # TARGET T0399 # 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 T0399.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 78 # # ============================================ # Comments from T0399.t06.alpha.rdb # ============================================ # TARGET T0399 # 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 T0399.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 78 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 V 0.3432 0.0614 0.5954 2 T 0.2999 0.0631 0.6369 3 T 0.2763 0.1358 0.5880 4 D 0.2246 0.1374 0.6379 5 Q 0.1914 0.2823 0.5263 6 N 0.1478 0.2932 0.5590 7 H 0.2258 0.2101 0.5642 8 F 0.3167 0.0805 0.6029 9 S 0.2314 0.0990 0.6696 10 G 0.1854 0.1272 0.6874 11 G 0.1653 0.1058 0.7289 12 T 0.2188 0.0901 0.6911 13 S 0.1909 0.0666 0.7425 14 I 0.0131 0.7485 0.2384 15 E 0.0092 0.8624 0.1284 16 Q 0.0084 0.9170 0.0746 17 L 0.0092 0.9155 0.0753 18 K 0.0088 0.9034 0.0878 19 Q 0.0098 0.8839 0.1063 20 W 0.0191 0.7458 0.2350 21 F 0.0605 0.2751 0.6644 22 G 0.0538 0.1217 0.8245 23 D 0.1667 0.0439 0.7893 24 P 0.1586 0.1607 0.6807 25 N 0.1564 0.1668 0.6767 26 K 0.2267 0.1549 0.6184 27 S 0.3051 0.1666 0.5283 28 E 0.3400 0.1965 0.4635 29 Q 0.3413 0.2000 0.4586 30 R 0.2980 0.1895 0.5125 31 N 0.2455 0.1783 0.5763 32 A 0.1654 0.1430 0.6916 33 G 0.1384 0.0954 0.7662 34 N 0.3502 0.0500 0.5998 35 I 0.5828 0.0218 0.3954 36 T 0.6671 0.0201 0.3128 37 L 0.6905 0.0360 0.2735 38 D 0.6562 0.0516 0.2922 39 S 0.6792 0.0437 0.2771 40 Y 0.6305 0.0563 0.3132 41 T 0.6733 0.0406 0.2861 42 W 0.6206 0.0475 0.3318 43 V 0.4558 0.0799 0.4643 44 K 0.2300 0.1510 0.6190 45 D 0.1386 0.1042 0.7572 46 G 0.1659 0.0739 0.7601 47 A 0.5305 0.0345 0.4350 48 V 0.7324 0.0090 0.2586 49 I 0.7977 0.0065 0.1958 50 N 0.8154 0.0048 0.1798 51 A 0.8217 0.0047 0.1735 52 Q 0.8135 0.0052 0.1813 53 L 0.7566 0.0086 0.2348 54 Y 0.5155 0.0229 0.4616 55 K 0.1561 0.2136 0.6302 56 N 0.0933 0.1641 0.7426 57 S 0.2206 0.1425 0.6369 58 T 0.4213 0.1979 0.3807 59 V 0.4579 0.2715 0.2705 60 A 0.4218 0.3571 0.2211 61 R 0.3472 0.4473 0.2055 62 S 0.2596 0.4929 0.2475 63 I 0.2365 0.4172 0.3464 64 S 0.1444 0.3880 0.4676 65 N 0.1044 0.3192 0.5764 66 F 0.1673 0.2737 0.5589 67 S 0.1869 0.2940 0.5191 68 F 0.1870 0.2890 0.5240 69 S 0.1612 0.2821 0.5566 70 R 0.0969 0.4416 0.4615 71 E 0.1313 0.3603 0.5084 72 A 0.2328 0.2827 0.4845 73 K 0.3016 0.1489 0.5494 74 I 0.3685 0.0633 0.5682 75 G 0.2072 0.0260 0.7668 76 K 0.0314 0.6240 0.3446 77 E 0.0243 0.7089 0.2668 78 D 0.0450 0.6494 0.3056 79 Y 0.0484 0.7013 0.2503 80 D 0.0267 0.7344 0.2389 81 E 0.0427 0.6316 0.3257 82 L 0.1539 0.4493 0.3968 83 K 0.1258 0.4111 0.4631 84 I 0.1134 0.1963 0.6903 85 G 0.0626 0.1247 0.8128 86 E 0.1621 0.1044 0.7335 87 S 0.1802 0.0854 0.7344 88 Y 0.0201 0.7147 0.2652 89 K 0.0102 0.8632 0.1266 90 K 0.0093 0.9158 0.0749 91 V 0.0105 0.9164 0.0732 92 V 0.0091 0.9123 0.0786 93 E 0.0107 0.8952 0.0941 94 K 0.0208 0.7727 0.2065 95 L 0.0650 0.3022 0.6328 96 G 0.0492 0.1006 0.8502 97 E 0.1718 0.0381 0.7900 98 P 0.1725 0.1063 0.7212 99 D 0.1774 0.1619 0.6607 100 V 0.3446 0.1831 0.4723 101 L 0.4698 0.1538 0.3764 102 S 0.4863 0.1631 0.3506 103 Q 0.4668 0.1772 0.3559 104 S 0.4147 0.1660 0.4194 105 M 0.3355 0.1494 0.5151 106 S 0.2531 0.1284 0.6184 107 S 0.1504 0.1862 0.6634 108 D 0.1403 0.1578 0.7019 109 K 0.2510 0.1646 0.5844 110 E 0.4286 0.1220 0.4493 111 E 0.5985 0.0650 0.3365 112 M 0.6864 0.0439 0.2697 113 Q 0.7449 0.0308 0.2243 114 T 0.7843 0.0162 0.1995 115 V 0.7716 0.0222 0.2061 116 W 0.7149 0.0382 0.2470 117 S 0.5724 0.0963 0.3313 118 S 0.3250 0.1462 0.5288 119 G 0.2069 0.1223 0.6708 120 I 0.2551 0.1033 0.6416 121 K 0.2395 0.1155 0.6450 122 T 0.2089 0.1088 0.6822 123 K 0.1701 0.1478 0.6821 124 S 0.2070 0.0950 0.6980 125 S 0.1817 0.1886 0.6297 126 S 0.2596 0.1151 0.6253 127 A 0.5878 0.0480 0.3642 128 T 0.7523 0.0110 0.2368 129 I 0.8168 0.0049 0.1783 130 E 0.8160 0.0047 0.1794 131 L 0.8201 0.0047 0.1752 132 Y 0.8132 0.0056 0.1812 133 F 0.7245 0.0138 0.2617 134 E 0.5496 0.1175 0.3329 135 N 0.1778 0.0828 0.7394 136 G 0.1161 0.0630 0.8209 137 L 0.5055 0.0244 0.4702 138 L 0.6618 0.0189 0.3193 139 K 0.6442 0.0430 0.3128 140 N 0.5995 0.0567 0.3438 141 K 0.4806 0.1555 0.3639 142 T 0.4116 0.1542 0.4342 143 Q 0.2565 0.2875 0.4559 144 K 0.1599 0.3421 0.4980 145 D 0.1181 0.2609 0.6209 146 L 0.1797 0.2034 0.6169 147 E 0.1773 0.2086 0.6141