# This file is the result of combining several RDB files, specifically # T0399.t04.str2.rdb (weight 1.54425) # T0399.t04.str4.rdb (weight 0.924988) # T0399.t04.pb.rdb (weight 0.789901) # T0399.t04.bys.rdb (weight 0.748322) # T0399.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 T0399.t04.str2.rdb # ============================================ # TARGET T0399 # 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 T0399.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 55 # # ============================================ # Comments from T0399.t04.str4.rdb # ============================================ # TARGET T0399 # 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 T0399.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 55 # # ============================================ # Comments from T0399.t04.pb.rdb # ============================================ # TARGET T0399 # 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 T0399.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 55 # # ============================================ # Comments from T0399.t04.bys.rdb # ============================================ # TARGET T0399 # 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 T0399.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 55 # # ============================================ # Comments from T0399.t04.alpha.rdb # ============================================ # TARGET T0399 # 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 T0399.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 55 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 V 0.3919 0.0412 0.5669 2 T 0.3178 0.0430 0.6392 3 T 0.3171 0.1782 0.5047 4 D 0.2470 0.1664 0.5866 5 Q 0.2330 0.2325 0.5345 6 N 0.2492 0.1620 0.5889 7 H 0.3735 0.1066 0.5200 8 F 0.4161 0.0763 0.5076 9 S 0.2991 0.0959 0.6050 10 G 0.1825 0.1424 0.6752 11 G 0.1528 0.1238 0.7234 12 T 0.2012 0.1041 0.6947 13 S 0.1946 0.0684 0.7370 14 I 0.0139 0.7345 0.2517 15 E 0.0096 0.8655 0.1250 16 Q 0.0089 0.9174 0.0737 17 L 0.0085 0.9165 0.0750 18 K 0.0089 0.9141 0.0770 19 Q 0.0102 0.8769 0.1129 20 W 0.0172 0.7738 0.2090 21 F 0.0643 0.3080 0.6277 22 G 0.0574 0.1388 0.8037 23 D 0.1641 0.0397 0.7963 24 P 0.1260 0.2174 0.6566 25 N 0.1305 0.1814 0.6881 26 K 0.2060 0.1729 0.6211 27 S 0.2420 0.1691 0.5889 28 E 0.2407 0.2302 0.5291 29 Q 0.2617 0.2343 0.5040 30 R 0.2652 0.2011 0.5336 31 N 0.2224 0.1656 0.6120 32 A 0.1702 0.1505 0.6793 33 G 0.1265 0.1125 0.7610 34 N 0.2579 0.0761 0.6660 35 I 0.4961 0.0316 0.4723 36 T 0.6058 0.0304 0.3638 37 L 0.6402 0.0465 0.3133 38 D 0.5676 0.0779 0.3545 39 S 0.5956 0.0607 0.3437 40 Y 0.5595 0.0659 0.3746 41 T 0.5945 0.0533 0.3522 42 W 0.5376 0.0554 0.4070 43 V 0.3935 0.0674 0.5391 44 K 0.2293 0.1435 0.6272 45 D 0.1305 0.1046 0.7648 46 G 0.1533 0.0589 0.7877 47 A 0.5216 0.0148 0.4636 48 V 0.7486 0.0067 0.2447 49 I 0.8078 0.0057 0.1865 50 N 0.8248 0.0042 0.1710 51 A 0.8228 0.0047 0.1725 52 Q 0.8152 0.0047 0.1801 53 L 0.7343 0.0106 0.2551 54 Y 0.5018 0.0332 0.4650 55 K 0.1947 0.1343 0.6710 56 N 0.1269 0.1453 0.7277 57 S 0.2649 0.1504 0.5847 58 T 0.4270 0.1671 0.4059 59 V 0.4898 0.1807 0.3295 60 A 0.4427 0.2400 0.3172 61 R 0.2902 0.4382 0.2716 62 S 0.2423 0.4593 0.2984 63 I 0.2085 0.4107 0.3808 64 S 0.1609 0.3278 0.5112 65 N 0.1463 0.2448 0.6089 66 F 0.2549 0.1593 0.5858 67 S 0.2740 0.1972 0.5288 68 F 0.2732 0.2626 0.4641 69 S 0.2059 0.2678 0.5264 70 R 0.1375 0.3443 0.5182 71 E 0.1544 0.2959 0.5497 72 A 0.2506 0.2205 0.5289 73 K 0.2868 0.1905 0.5227 74 I 0.3524 0.1243 0.5233 75 G 0.2027 0.0580 0.7393 76 K 0.0347 0.6692 0.2961 77 E 0.0222 0.7721 0.2057 78 D 0.0468 0.6676 0.2856 79 Y 0.0423 0.7165 0.2412 80 D 0.0354 0.7238 0.2408 81 E 0.0852 0.5992 0.3157 82 L 0.1850 0.4582 0.3568 83 K 0.1990 0.3610 0.4400 84 I 0.1401 0.2431 0.6169 85 G 0.0740 0.1400 0.7859 86 E 0.1654 0.1515 0.6832 87 S 0.1969 0.1751 0.6280 88 Y 0.0243 0.7007 0.2750 89 K 0.0112 0.8508 0.1380 90 K 0.0131 0.9048 0.0821 91 V 0.0113 0.9149 0.0738 92 V 0.0109 0.9069 0.0823 93 E 0.0127 0.8794 0.1079 94 K 0.0211 0.7687 0.2102 95 L 0.0713 0.3421 0.5867 96 G 0.0644 0.1431 0.7925 97 E 0.1663 0.0489 0.7848 98 P 0.1720 0.1434 0.6845 99 D 0.1880 0.2206 0.5914 100 V 0.2817 0.2446 0.4737 101 L 0.3184 0.2783 0.4033 102 S 0.3340 0.2937 0.3723 103 Q 0.3373 0.2932 0.3695 104 S 0.3544 0.2020 0.4436 105 M 0.2880 0.1830 0.5290 106 S 0.2223 0.1525 0.6252 107 S 0.1681 0.1609 0.6710 108 D 0.1402 0.1320 0.7277 109 K 0.1976 0.1849 0.6175 110 E 0.3640 0.1481 0.4879 111 E 0.5724 0.0851 0.3425 112 M 0.6881 0.0479 0.2639 113 Q 0.7532 0.0355 0.2113 114 T 0.7855 0.0187 0.1958 115 V 0.7878 0.0183 0.1939 116 W 0.7153 0.0336 0.2511 117 S 0.5439 0.1076 0.3485 118 S 0.2344 0.1364 0.6292 119 G 0.1261 0.0949 0.7790 120 I 0.2296 0.1173 0.6531 121 K 0.2600 0.1304 0.6096 122 T 0.2310 0.1185 0.6505 123 K 0.1919 0.1336 0.6745 124 S 0.2202 0.1208 0.6591 125 S 0.2066 0.1392 0.6542 126 S 0.2860 0.0664 0.6475 127 A 0.5514 0.0231 0.4255 128 T 0.7479 0.0117 0.2404 129 I 0.8201 0.0047 0.1751 130 E 0.8284 0.0043 0.1673 131 L 0.8224 0.0044 0.1732 132 Y 0.8192 0.0055 0.1753 133 F 0.7442 0.0080 0.2478 134 E 0.5870 0.0584 0.3546 135 N 0.2124 0.0602 0.7273 136 G 0.1638 0.0632 0.7729 137 L 0.5032 0.0379 0.4589 138 L 0.6766 0.0301 0.2932 139 K 0.6479 0.0530 0.2991 140 N 0.6449 0.0639 0.2913 141 K 0.5194 0.1503 0.3303 142 T 0.4125 0.1986 0.3889 143 Q 0.2880 0.2512 0.4608 144 K 0.1810 0.2240 0.5950 145 D 0.1637 0.1502 0.6861 146 L 0.2232 0.1418 0.6350 147 E 0.2210 0.1588 0.6202