# This file is the result of combining several RDB files, specifically # T0630.t04.str2.rdb (weight 1.54425) # T0630.t04.str4.rdb (weight 0.924988) # T0630.t04.pb.rdb (weight 0.789901) # T0630.t04.bys.rdb (weight 0.748322) # T0630.t04.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 T0630.t04.str2.rdb # ============================================ # TARGET T0630 # 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 T0630.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 302 # # ============================================ # Comments from T0630.t04.str4.rdb # ============================================ # TARGET T0630 # 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 T0630.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 302 # # ============================================ # Comments from T0630.t04.pb.rdb # ============================================ # TARGET T0630 # 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 T0630.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 302 # # ============================================ # Comments from T0630.t04.bys.rdb # ============================================ # TARGET T0630 # 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 T0630.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 302 # # ============================================ # Comments from T0630.t04.alpha.rdb # ============================================ # TARGET T0630 # 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 T0630.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 302 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.2581 0.1018 0.6401 2 R 0.2742 0.0825 0.6433 3 A 0.3040 0.0446 0.6514 4 P 0.2408 0.0722 0.6870 5 I 0.2704 0.0649 0.6647 6 P 0.2322 0.0803 0.6875 7 E 0.2929 0.0467 0.6604 8 P 0.2622 0.0363 0.7015 9 K 0.2258 0.0223 0.7519 10 P 0.1779 0.1733 0.6488 11 G 0.1720 0.1342 0.6938 12 D 0.4033 0.0793 0.5175 13 L 0.6646 0.0495 0.2859 14 I 0.7662 0.0206 0.2132 15 E 0.7736 0.0142 0.2123 16 I 0.7080 0.0282 0.2638 17 F 0.5026 0.0701 0.4273 18 R 0.3757 0.0637 0.5606 19 P 0.2586 0.1872 0.5542 20 F 0.3078 0.1849 0.5072 21 Y 0.3815 0.1380 0.4805 22 R 0.4720 0.1021 0.4260 23 H 0.6206 0.0448 0.3347 24 W 0.6933 0.0425 0.2643 25 A 0.7938 0.0085 0.1977 26 I 0.8094 0.0073 0.1833 27 Y 0.7870 0.0066 0.2064 28 V 0.6648 0.0284 0.3068 29 G 0.4121 0.0473 0.5406 30 D 0.1666 0.0920 0.7414 31 G 0.1599 0.0553 0.7848 32 Y 0.5364 0.0215 0.4422 33 V 0.7054 0.0093 0.2853 34 V 0.7585 0.0106 0.2309 35 H 0.7709 0.0088 0.2203 36 L 0.7083 0.0141 0.2776 37 A 0.5186 0.0178 0.4636 38 P 0.2263 0.0210 0.7527 39 P 0.1334 0.2795 0.5871 40 S 0.0927 0.3114 0.5960 41 E 0.1369 0.3839 0.4792 42 V 0.2039 0.2987 0.4974 43 A 0.1771 0.2830 0.5398 44 G 0.1339 0.2020 0.6641 45 A 0.1635 0.1811 0.6554 46 G 0.1528 0.1446 0.7026 47 A 0.1602 0.2751 0.5647 48 A 0.1781 0.3512 0.4707 49 S 0.2398 0.3797 0.3805 50 V 0.2389 0.4481 0.3130 51 M 0.2404 0.4638 0.2958 52 S 0.1772 0.5285 0.2943 53 A 0.1275 0.5668 0.3058 54 L 0.1434 0.4329 0.4237 55 T 0.1416 0.3448 0.5136 56 D 0.1267 0.2516 0.6216 57 K 0.1961 0.2133 0.5905 58 A 0.3511 0.1532 0.4956 59 I 0.5092 0.1345 0.3563 60 V 0.5341 0.1247 0.3412 61 K 0.4231 0.1817 0.3952 62 K 0.2884 0.3392 0.3724 63 E 0.2335 0.4096 0.3568 64 L 0.2021 0.4597 0.3382 65 L 0.0962 0.6571 0.2467 66 Y 0.0947 0.7053 0.2000 67 D 0.1225 0.6813 0.1961 68 V 0.1664 0.5584 0.2751 69 A 0.2121 0.3272 0.4607 70 G 0.1448 0.1840 0.6711 71 S 0.1773 0.1184 0.7042 72 D 0.2214 0.1117 0.6669 73 K 0.4132 0.0829 0.5039 74 Y 0.6524 0.0276 0.3200 75 Q 0.7226 0.0182 0.2592 76 V 0.7010 0.0314 0.2676 77 N 0.5211 0.0795 0.3994 78 N 0.3502 0.0895 0.5602 79 K 0.2677 0.1467 0.5856 80 H 0.2267 0.1550 0.6183 81 D 0.1697 0.1735 0.6569 82 D 0.1516 0.2171 0.6312 83 K 0.2437 0.1750 0.5812 84 Y 0.3001 0.0976 0.6023 85 S 0.2830 0.0403 0.6767 86 P 0.2485 0.0846 0.6670 87 L 0.2299 0.0462 0.7238 88 P 0.1516 0.1235 0.7249 89 C 0.0387 0.5617 0.3996 90 S 0.0187 0.7865 0.1948 91 K 0.0282 0.8676 0.1041 92 I 0.0209 0.8982 0.0809 93 I 0.0097 0.9185 0.0718 94 Q 0.0091 0.9215 0.0694 95 R 0.0094 0.9197 0.0709 96 A 0.0091 0.9150 0.0759 97 E 0.0091 0.9132 0.0777 98 E 0.0097 0.8917 0.0987 99 L 0.0184 0.7856 0.1960 100 V 0.0612 0.4353 0.5035 101 G 0.0497 0.2239 0.7264 102 Q 0.1395 0.2136 0.6469 103 E 0.2186 0.2061 0.5753 104 V 0.3141 0.1632 0.5227 105 L 0.3553 0.1609 0.4838 106 Y 0.4452 0.1204 0.4343 107 K 0.4255 0.1396 0.4349 108 L 0.3706 0.2528 0.3766 109 T 0.2704 0.3332 0.3964 110 S 0.1598 0.4762 0.3641 111 E 0.0998 0.4955 0.4047 112 N 0.1015 0.4596 0.4389 113 C 0.0654 0.6764 0.2582 114 E 0.0315 0.8303 0.1383 115 H 0.0326 0.8459 0.1215 116 F 0.0309 0.8718 0.0973 117 V 0.0191 0.8908 0.0901 118 N 0.0190 0.8940 0.0870 119 E 0.0418 0.8388 0.1195 120 L 0.0571 0.7871 0.1558 121 R 0.0731 0.6554 0.2715 122 Y 0.0984 0.3103 0.5914 123 G 0.0967 0.1497 0.7536 124 V 0.2086 0.1139 0.6775 125 A 0.2258 0.1503 0.6239 126 R 0.2160 0.1943 0.5897 127 S 0.1936 0.2615 0.5448 128 D 0.0915 0.4856 0.4230 129 Q 0.1890 0.4172 0.3938 130 V 0.2932 0.2475 0.4593 131 R 0.2209 0.2206 0.5584 132 D 0.1834 0.1631 0.6535