# This file is the result of combining several RDB files, specifically # T0471.t04.str2.rdb (weight 1.54425) # T0471.t04.str4.rdb (weight 0.924988) # T0471.t04.pb.rdb (weight 0.789901) # T0471.t04.bys.rdb (weight 0.748322) # T0471.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 T0471.t04.str2.rdb # ============================================ # TARGET T0471 # 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 T0471.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 13.2214 # # ============================================ # Comments from T0471.t04.str4.rdb # ============================================ # TARGET T0471 # 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 T0471.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 13.2214 # # ============================================ # Comments from T0471.t04.pb.rdb # ============================================ # TARGET T0471 # 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 T0471.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 13.2214 # # ============================================ # Comments from T0471.t04.bys.rdb # ============================================ # TARGET T0471 # 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 T0471.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 13.2214 # # ============================================ # Comments from T0471.t04.alpha.rdb # ============================================ # TARGET T0471 # 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 T0471.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 13.2214 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.1255 0.4310 0.4436 2 W 0.0775 0.5750 0.3475 3 N 0.0342 0.7514 0.2144 4 D 0.0255 0.8179 0.1566 5 L 0.0160 0.8568 0.1272 6 A 0.0108 0.9013 0.0879 7 V 0.0108 0.9142 0.0750 8 Y 0.0133 0.9085 0.0782 9 I 0.0218 0.8829 0.0953 10 I 0.0318 0.8353 0.1330 11 R 0.0699 0.6965 0.2336 12 C 0.1084 0.4264 0.4652 13 S 0.1416 0.1849 0.6735 14 G 0.1358 0.0873 0.7769 15 P 0.1024 0.1798 0.7177 16 G 0.0795 0.1020 0.8184 17 T 0.2762 0.0346 0.6893 18 R 0.5227 0.0221 0.4552 19 V 0.7698 0.0076 0.2226 20 V 0.7821 0.0092 0.2086 21 E 0.7689 0.0062 0.2249 22 V 0.7311 0.0211 0.2478 23 G 0.5916 0.0370 0.3714 24 A 0.3990 0.1141 0.4869 25 G 0.2467 0.1508 0.6025 26 R 0.2245 0.2822 0.4932 27 F 0.1297 0.4961 0.3742 28 L 0.0466 0.7385 0.2148 29 Y 0.0389 0.8029 0.1582 30 V 0.0131 0.8729 0.1140 31 S 0.0092 0.9028 0.0881 32 D 0.0085 0.9087 0.0828 33 Y 0.0088 0.9001 0.0911 34 I 0.0107 0.8830 0.1063 35 R 0.0151 0.7822 0.2027 36 K 0.0227 0.6544 0.3229 37 H 0.0822 0.4211 0.4967 38 S 0.0751 0.2352 0.6897 39 K 0.0779 0.0846 0.8375 40 V 0.2742 0.0192 0.7066 41 D 0.5779 0.0246 0.3975 42 L 0.7844 0.0066 0.2090 43 V 0.7687 0.0115 0.2199 44 L 0.7623 0.0069 0.2308 45 T 0.7463 0.0149 0.2387 46 D 0.6515 0.0188 0.3297 47 I 0.4451 0.0423 0.5125 48 K 0.2992 0.0313 0.6695 49 P 0.2333 0.0956 0.6711 50 S 0.1486 0.2154 0.6360 51 H 0.1327 0.1895 0.6778 52 G 0.1403 0.1188 0.7408 53 G 0.1965 0.0792 0.7243 54 I 0.4299 0.0454 0.5247 55 V 0.5780 0.0473 0.3747 56 R 0.5333 0.0847 0.3820 57 D 0.3759 0.1468 0.4772 58 D 0.2875 0.1910 0.5215 59 I 0.2091 0.2587 0.5322 60 T 0.1997 0.1802 0.6201 61 S 0.2223 0.1069 0.6709 62 P 0.1107 0.3252 0.5641 63 R 0.1510 0.2383 0.6106 64 M 0.3135 0.2056 0.4810 65 E 0.4341 0.2142 0.3517 66 I 0.4437 0.2709 0.2854 67 Y 0.4240 0.2463 0.3298 68 R 0.2544 0.2443 0.5014 69 G 0.1475 0.1189 0.7336 70 A 0.3506 0.0796 0.5698 71 A 0.5120 0.0736 0.4144 72 L 0.7482 0.0343 0.2175 73 I 0.7349 0.0312 0.2339 74 Y 0.7671 0.0171 0.2158 75 S 0.7287 0.0266 0.2447 76 I 0.5618 0.0511 0.3871 77 R 0.3115 0.0266 0.6618 78 P 0.1669 0.0210 0.8120 79 P 0.1394 0.1891 0.6714 80 A 0.0193 0.7042 0.2765 81 E 0.0204 0.7725 0.2071 82 I 0.0283 0.7644 0.2073 83 H 0.0221 0.8327 0.1452 84 S 0.0133 0.8816 0.1051 85 S 0.0106 0.8984 0.0910 86 L 0.0096 0.9106 0.0798 87 M 0.0088 0.9163 0.0749 88 R 0.0086 0.9191 0.0723 89 V 0.0089 0.9081 0.0830 90 A 0.0096 0.8976 0.0928 91 D 0.0109 0.8496 0.1395 92 A 0.0239 0.7327 0.2434 93 V 0.0804 0.3242 0.5954 94 G 0.0747 0.0964 0.8288 95 A 0.2573 0.0301 0.7126 96 R 0.4097 0.0387 0.5516 97 L 0.7819 0.0068 0.2113 98 I 0.7725 0.0099 0.2176 99 I 0.7671 0.0080 0.2249 100 K 0.6969 0.0155 0.2876 101 P 0.4705 0.0349 0.4946 102 L 0.2653 0.1163 0.6184 103 T 0.1504 0.1172 0.7324 104 G 0.0961 0.1153 0.7886 105 E 0.1929 0.1618 0.6453 106 D 0.3186 0.1562 0.5252 107 I 0.3790 0.1765 0.4446 108 V 0.3998 0.1481 0.4521 109 T 0.3464 0.1407 0.5129 110 E 0.2292 0.2253 0.5455 111 R 0.1781 0.2375 0.5844 112 K 0.2331 0.1484 0.6185 113 M 0.4002 0.0477 0.5522 114 K 0.5527 0.0424 0.4049 115 L 0.6609 0.0345 0.3046 116 V 0.6150 0.0496 0.3355 117 N 0.4821 0.0519 0.4660 118 Y 0.2632 0.1116 0.6252 119 G 0.1651 0.0915 0.7433 120 R 0.2795 0.0866 0.6339 121 T 0.5127 0.0638 0.4235 122 Y 0.6980 0.0428 0.2592 123 F 0.7557 0.0367 0.2076 124 Y 0.7734 0.0308 0.1958 125 E 0.7479 0.0544 0.1977 126 Y 0.6815 0.0881 0.2304 127 I 0.5356 0.1832 0.2813 128 A 0.2406 0.4434 0.3160 129 E 0.1601 0.5194 0.3205 130 V 0.1937 0.4422 0.3642 131 R 0.2037 0.3123 0.4839 132 S 0.1710 0.2546 0.5744 133 R 0.1722 0.2061 0.6218