# This file is the result of combining several RDB files, specifically # T0397.t2k.str2.rdb (weight 1.54425) # T0397.t2k.str4.rdb (weight 0.924988) # T0397.t2k.pb.rdb (weight 0.789901) # T0397.t2k.bys.rdb (weight 0.748322) # T0397.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 T0397.t2k.str2.rdb # ============================================ # TARGET T0397 # 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 T0397.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 10.2986 # # ============================================ # Comments from T0397.t2k.str4.rdb # ============================================ # TARGET T0397 # 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 T0397.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 10.2986 # # ============================================ # Comments from T0397.t2k.pb.rdb # ============================================ # TARGET T0397 # 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 T0397.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 10.2986 # # ============================================ # Comments from T0397.t2k.bys.rdb # ============================================ # TARGET T0397 # 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 T0397.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 10.2986 # # ============================================ # Comments from T0397.t2k.alpha.rdb # ============================================ # TARGET T0397 # 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 T0397.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 10.2986 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.4105 0.0603 0.5292 2 K 0.4178 0.0414 0.5408 3 I 0.4688 0.0200 0.5112 4 P 0.4152 0.0333 0.5515 5 K 0.6795 0.0165 0.3041 6 I 0.7622 0.0070 0.2308 7 Y 0.7885 0.0064 0.2051 8 V 0.7656 0.0077 0.2267 9 E 0.7221 0.0159 0.2620 10 G 0.5990 0.0253 0.3757 11 E 0.5220 0.0447 0.4333 12 L 0.4213 0.0810 0.4977 13 N 0.3097 0.0844 0.6059 14 D 0.1745 0.1798 0.6457 15 G 0.1208 0.1569 0.7222 16 D 0.3177 0.1148 0.5675 17 R 0.5245 0.0839 0.3917 18 V 0.6332 0.0662 0.3006 19 A 0.6731 0.0544 0.2725 20 I 0.6406 0.0828 0.2765 21 E 0.4961 0.1214 0.3825 22 K 0.3037 0.1635 0.5328 23 D 0.1937 0.1140 0.6923 24 G 0.2673 0.0735 0.6592 25 N 0.5617 0.0251 0.4132 26 A 0.7275 0.0125 0.2599 27 I 0.7775 0.0113 0.2113 28 I 0.7731 0.0133 0.2136 29 F 0.7056 0.0260 0.2684 30 L 0.5137 0.0670 0.4192 31 E 0.3480 0.1037 0.5483 32 K 0.2124 0.2202 0.5675 33 D 0.1843 0.2517 0.5641 34 E 0.1304 0.4640 0.4056 35 E 0.1491 0.4339 0.4170 36 Y 0.2009 0.3105 0.4886 37 S 0.1630 0.2501 0.5869 38 G 0.1110 0.2059 0.6831 39 N 0.1126 0.2059 0.6814 40 G 0.1410 0.2332 0.6258 41 K 0.3008 0.2587 0.4405 42 L 0.3962 0.2864 0.3175 43 L 0.2537 0.4873 0.2590 44 Y 0.1918 0.6107 0.1974 45 Q 0.1595 0.6749 0.1656 46 V 0.1351 0.7045 0.1604 47 I 0.0789 0.7634 0.1576 48 Y 0.0288 0.8501 0.1211 49 D 0.0134 0.8871 0.0995 50 D 0.0113 0.8848 0.1039 51 L 0.0121 0.8745 0.1134 52 A 0.0118 0.8846 0.1036 53 K 0.0157 0.8541 0.1302 54 Y 0.0342 0.7437 0.2221 55 M 0.1283 0.5595 0.3122 56 S 0.1426 0.3835 0.4739 57 L 0.0467 0.5688 0.3845 58 D 0.0505 0.5301 0.4194 59 T 0.1382 0.3693 0.4925 60 L 0.2447 0.1950 0.5603 61 K 0.3142 0.1011 0.5847 62 K 0.3529 0.0899 0.5572 63 D 0.5219 0.0372 0.4409 64 V 0.7754 0.0071 0.2176 65 L 0.7933 0.0057 0.2010 66 I 0.8073 0.0052 0.1875 67 Q 0.7321 0.0080 0.2600 68 Y 0.4346 0.0159 0.5495 69 P 0.2042 0.1143 0.6815 70 D 0.1465 0.1333 0.7202 71 K 0.1596 0.1680 0.6724 72 H 0.3226 0.0978 0.5795 73 T 0.5533 0.0466 0.4001 74 L 0.7229 0.0205 0.2566 75 T 0.7835 0.0135 0.2030 76 Y 0.7853 0.0109 0.2039 77 L 0.7385 0.0195 0.2420 78 K 0.6295 0.0315 0.3391 79 A 0.2971 0.0657 0.6373 80 G 0.0960 0.0852 0.8188 81 T 0.3272 0.0487 0.6241 82 K 0.5632 0.0283 0.4085 83 L 0.7027 0.0195 0.2778 84 I 0.7524 0.0118 0.2358 85 S 0.7291 0.0078 0.2631 86 V 0.6869 0.0128 0.3003 87 P 0.5976 0.0101 0.3923 88 A 0.4388 0.0493 0.5119 89 E 0.3388 0.0645 0.5967 90 G 0.3011 0.0690 0.6300 91 Y 0.5074 0.0264 0.4662 92 K 0.6433 0.0175 0.3391 93 V 0.6316 0.0250 0.3434 94 Y 0.6371 0.0140 0.3490 95 P 0.5998 0.0172 0.3830 96 I 0.6788 0.0225 0.2988 97 M 0.6051 0.0417 0.3532 98 D 0.4341 0.0578 0.5082 99 F 0.2609 0.1652 0.5739 100 G 0.1873 0.1196 0.6931 101 F 0.3258 0.1761 0.4982 102 R 0.5090 0.1628 0.3282 103 V 0.5185 0.1775 0.3040 104 L 0.4508 0.1581 0.3911 105 K 0.2699 0.1383 0.5918 106 G 0.1298 0.0983 0.7718 107 Y 0.3410 0.0861 0.5728 108 R 0.5539 0.1048 0.3414 109 L 0.6508 0.0868 0.2624 110 A 0.7362 0.0522 0.2116 111 T 0.7622 0.0326 0.2052 112 L 0.7506 0.0390 0.2104 113 E 0.7008 0.0382 0.2609 114 S 0.5247 0.0378 0.4374 115 K 0.2977 0.1477 0.5546 116 K 0.1859 0.1090 0.7051 117 G 0.2134 0.0803 0.7063 118 D 0.5072 0.0228 0.4699 119 L 0.7115 0.0101 0.2784 120 R 0.7162 0.0142 0.2696 121 Y 0.7686 0.0096 0.2218 122 V 0.7033 0.0175 0.2792 123 N 0.6172 0.0220 0.3608 124 S 0.4113 0.0294 0.5593 125 P 0.2736 0.1230 0.6033 126 V 0.3166 0.1049 0.5785 127 S 0.2828 0.0788 0.6384 128 G 0.3966 0.0400 0.5633 129 T 0.7248 0.0079 0.2674 130 V 0.7952 0.0051 0.1997 131 I 0.8136 0.0054 0.1809 132 F 0.7960 0.0049 0.1991 133 M 0.7401 0.0153 0.2446 134 N 0.6351 0.0344 0.3304 135 E 0.4973 0.0562 0.4465 136 I 0.3622 0.0373 0.6005 137 P 0.2184 0.0878 0.6938 138 S 0.1284 0.2734 0.5982 139 E 0.1570 0.2164 0.6266 140 R 0.2084 0.1552 0.6364 141 A 0.2262 0.1674 0.6064 142 N 0.3395 0.0838 0.5767 143 Y 0.6384 0.0206 0.3410 144 V 0.7691 0.0072 0.2236 145 F 0.8172 0.0049 0.1779 146 Y 0.8183 0.0051 0.1766 147 M 0.7932 0.0061 0.2007 148 L 0.7109 0.0097 0.2793 149 E 0.5104 0.0167 0.4729 150 E 0.3074 0.1073 0.5853