# This file is the result of combining several RDB files, specifically # T0495.t2k.str2.rdb (weight 1.54425) # T0495.t2k.str4.rdb (weight 0.924988) # T0495.t2k.pb.rdb (weight 0.789901) # T0495.t2k.bys.rdb (weight 0.748322) # T0495.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 T0495.t2k.str2.rdb # ============================================ # TARGET T0495 # 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 T0495.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 13.8477 # # ============================================ # Comments from T0495.t2k.str4.rdb # ============================================ # TARGET T0495 # 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 T0495.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 13.8477 # # ============================================ # Comments from T0495.t2k.pb.rdb # ============================================ # TARGET T0495 # 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 T0495.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 13.8477 # # ============================================ # Comments from T0495.t2k.bys.rdb # ============================================ # TARGET T0495 # 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 T0495.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 13.8477 # # ============================================ # Comments from T0495.t2k.alpha.rdb # ============================================ # TARGET T0495 # 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 T0495.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 13.8477 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.2658 0.0490 0.6852 2 P 0.1869 0.1516 0.6616 3 M 0.1605 0.2432 0.5962 4 T 0.1608 0.2826 0.5566 5 L 0.1437 0.3210 0.5353 6 D 0.1738 0.2631 0.5631 7 L 0.1772 0.2641 0.5587 8 Q 0.1655 0.2171 0.6174 9 P 0.0588 0.6553 0.2859 10 G 0.0335 0.7947 0.1718 11 Q 0.0277 0.8635 0.1089 12 R 0.0217 0.8861 0.0921 13 L 0.0163 0.8943 0.0895 14 A 0.0155 0.8873 0.0972 15 R 0.0138 0.8856 0.1006 16 G 0.0142 0.8754 0.1104 17 V 0.0109 0.8994 0.0897 18 A 0.0089 0.9148 0.0763 19 R 0.0088 0.9201 0.0711 20 H 0.0092 0.9170 0.0738 21 L 0.0099 0.9054 0.0848 22 R 0.0105 0.8592 0.1303 23 A 0.0199 0.7295 0.2506 24 H 0.0582 0.2405 0.7013 25 G 0.0558 0.0815 0.8628 26 F 0.2992 0.0514 0.6494 27 V 0.5774 0.0343 0.3883 28 S 0.6621 0.0263 0.3116 29 V 0.5737 0.0783 0.3479 30 E 0.4825 0.1495 0.3680 31 E 0.5093 0.1353 0.3554 32 F 0.4711 0.0687 0.4602 33 V 0.4014 0.0357 0.5629 34 P 0.2486 0.0969 0.6545 35 A 0.1349 0.3021 0.5630 36 R 0.0896 0.1969 0.7135 37 G 0.0851 0.1042 0.8107 38 L 0.2882 0.0496 0.6621 39 R 0.4890 0.0420 0.4690 40 V 0.5505 0.0400 0.4095 41 D 0.6029 0.0403 0.3568 42 V 0.7419 0.0449 0.2132 43 M 0.7100 0.0471 0.2429 44 G 0.7059 0.0382 0.2559 45 L 0.6079 0.0466 0.3456 46 G 0.2874 0.0274 0.6852 47 P 0.1602 0.2322 0.6076 48 K 0.1011 0.1477 0.7511 49 G 0.1668 0.0689 0.7644 50 E 0.4647 0.0137 0.5216 51 I 0.7357 0.0061 0.2582 52 W 0.8101 0.0052 0.1847 53 V 0.8247 0.0042 0.1711 54 I 0.8162 0.0054 0.1784 55 E 0.8108 0.0047 0.1844 56 C 0.7782 0.0057 0.2160 57 K 0.6288 0.0207 0.3505 58 S 0.4360 0.0425 0.5214 59 S 0.2251 0.0674 0.7075 60 R 0.0865 0.4758 0.4377 61 A 0.0691 0.6113 0.3196 62 D 0.0862 0.6196 0.2942 63 F 0.0789 0.6853 0.2359 64 Q 0.0858 0.6424 0.2718 65 A 0.0953 0.5799 0.3247 66 D 0.1208 0.4305 0.4487 67 A 0.0389 0.6259 0.3353 68 K 0.0515 0.5180 0.4305 69 W 0.0803 0.5066 0.4131 70 Q 0.0431 0.6014 0.3554 71 G 0.0406 0.4951 0.4643 72 Y 0.0633 0.5829 0.3538 73 L 0.0831 0.6236 0.2933 74 E 0.0612 0.6600 0.2788 75 W 0.0880 0.5616 0.3504 76 C 0.1445 0.5127 0.3427 77 D 0.1534 0.4990 0.3476 78 R 0.2416 0.4294 0.3290 79 Y 0.4263 0.2596 0.3141 80 F 0.5649 0.1700 0.2652 81 W 0.6198 0.1112 0.2690 82 A 0.5902 0.0894 0.3204 83 V 0.4733 0.0747 0.4520 84 D 0.2906 0.0834 0.6260 85 M 0.0893 0.3574 0.5533 86 E 0.1416 0.2324 0.6260 87 F 0.2880 0.0456 0.6664 88 P 0.2052 0.0926 0.7022 89 A 0.0930 0.4936 0.4133 90 E 0.0988 0.5185 0.3827 91 L 0.2153 0.2545 0.5302 92 L 0.2559 0.0651 0.6790 93 P 0.1872 0.1289 0.6839 94 A 0.0661 0.3875 0.5464 95 E 0.1137 0.3294 0.5569 96 S 0.2203 0.1559 0.6238 97 G 0.3863 0.0757 0.5379 98 L 0.7217 0.0185 0.2597 99 L 0.7614 0.0124 0.2262 100 I 0.7700 0.0151 0.2150 101 A 0.6256 0.0461 0.3284 102 D 0.4073 0.0869 0.5058 103 A 0.2454 0.2208 0.5339 104 Y 0.1987 0.1905 0.6108 105 D 0.2648 0.1354 0.5999 106 A 0.4670 0.1223 0.4106 107 E 0.6296 0.0921 0.2783 108 I 0.6572 0.1045 0.2383 109 V 0.6016 0.1224 0.2760 110 R 0.4961 0.1463 0.3576 111 M 0.3381 0.1261 0.5358 112 A 0.2579 0.0424 0.6997 113 P 0.1123 0.3035 0.5842 114 E 0.0814 0.4571 0.4615 115 Q 0.1086 0.4839 0.4074 116 K 0.0956 0.3983 0.5060 117 L 0.1443 0.2406 0.6151 118 A 0.1396 0.2001 0.6603 119 P 0.0727 0.5091 0.4183 120 A 0.0416 0.7172 0.2413 121 R 0.0298 0.7920 0.1782 122 R 0.0195 0.8541 0.1264 123 K 0.0125 0.8909 0.0965 124 V 0.0102 0.9078 0.0820 125 L 0.0090 0.9153 0.0757 126 I 0.0086 0.9173 0.0741 127 Q 0.0084 0.9175 0.0741 128 K 0.0083 0.9220 0.0697 129 F 0.0083 0.9222 0.0695 130 A 0.0083 0.9221 0.0696 131 T 0.0083 0.9230 0.0687 132 H 0.0083 0.9224 0.0693 133 A 0.0083 0.9204 0.0713 134 A 0.0083 0.9174 0.0742 135 R 0.0084 0.9144 0.0772 136 R 0.0087 0.9023 0.0890 137 L 0.0106 0.8852 0.1042 138 Q 0.0149 0.8387 0.1464 139 A 0.0308 0.7325 0.2367 140 L 0.0734 0.5364 0.3902 141 R 0.1580 0.3113 0.5307 142 D 0.1717 0.1116 0.7167 143 P 0.0321 0.4486 0.5193 144 E 0.0454 0.3150 0.6395 145 G 0.0871 0.2920 0.6209 146 H 0.1659 0.1810 0.6531 147 G 0.1944 0.1983 0.6073 148 I 0.2336 0.2186 0.5478 149 F 0.2566 0.1659 0.5775 150 E 0.2117 0.1799 0.6085