# This file is the result of combining several RDB files, specifically # T0425.t04.str2.rdb (weight 1.54425) # T0425.t04.str4.rdb (weight 0.924988) # T0425.t04.pb.rdb (weight 0.789901) # T0425.t04.bys.rdb (weight 0.748322) # T0425.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 T0425.t04.str2.rdb # ============================================ # TARGET T0425 # 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 T0425.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 201.785 # # ============================================ # Comments from T0425.t04.str4.rdb # ============================================ # TARGET T0425 # 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 T0425.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 201.785 # # ============================================ # Comments from T0425.t04.pb.rdb # ============================================ # TARGET T0425 # 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 T0425.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 201.785 # # ============================================ # Comments from T0425.t04.bys.rdb # ============================================ # TARGET T0425 # 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 T0425.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 201.785 # # ============================================ # Comments from T0425.t04.alpha.rdb # ============================================ # TARGET T0425 # 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 T0425.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 201.785 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.2336 0.0869 0.6795 2 S 0.2811 0.0552 0.6637 3 K 0.5498 0.0153 0.4349 4 I 0.7824 0.0068 0.2108 5 I 0.8062 0.0048 0.1890 6 C 0.8082 0.0050 0.1868 7 L 0.7887 0.0092 0.2022 8 T 0.6756 0.0095 0.3149 9 A 0.3520 0.1477 0.5003 10 G 0.1843 0.1154 0.7002 11 H 0.1622 0.1277 0.7101 12 S 0.1656 0.1465 0.6879 13 N 0.1818 0.1313 0.6869 14 T 0.2133 0.1453 0.6414 15 D 0.2289 0.0678 0.7033 16 P 0.1008 0.3356 0.5636 17 G 0.1190 0.2368 0.6442 18 A 0.2594 0.1837 0.5569 19 V 0.2955 0.1502 0.5543 20 N 0.2298 0.1188 0.6515 21 G 0.1371 0.1189 0.7440 22 S 0.1756 0.1323 0.6921 23 D 0.2108 0.2326 0.5566 24 R 0.1826 0.4080 0.4094 25 E 0.0802 0.6964 0.2234 26 A 0.0351 0.8221 0.1428 27 D 0.0335 0.8424 0.1241 28 L 0.0251 0.8756 0.0993 29 A 0.0105 0.9086 0.0809 30 Q 0.0083 0.9196 0.0720 31 D 0.0083 0.9234 0.0683 32 M 0.0083 0.9216 0.0700 33 R 0.0083 0.9233 0.0684 34 N 0.0083 0.9247 0.0670 35 I 0.0083 0.9245 0.0672 36 V 0.0083 0.9223 0.0694 37 A 0.0083 0.9233 0.0684 38 S 0.0083 0.9237 0.0681 39 I 0.0084 0.9192 0.0724 40 L 0.0087 0.9058 0.0855 41 R 0.0102 0.8568 0.1330 42 N 0.0157 0.7416 0.2427 43 D 0.0578 0.4598 0.4824 44 Y 0.0755 0.1595 0.7650 45 G 0.0851 0.0587 0.8562 46 L 0.3327 0.0125 0.6547 47 T 0.6057 0.0149 0.3794 48 V 0.7611 0.0061 0.2328 49 K 0.7527 0.0122 0.2351 50 T 0.7302 0.0073 0.2625 51 D 0.5744 0.0277 0.3979 52 G 0.3775 0.0530 0.5696 53 T 0.1889 0.1055 0.7056 54 G 0.1180 0.1118 0.7702 55 K 0.1431 0.1354 0.7215 56 G 0.2071 0.1274 0.6655 57 N 0.3130 0.0841 0.6030 58 M 0.3676 0.0646 0.5678 59 P 0.2402 0.0398 0.7199 60 L 0.0445 0.6132 0.3424 61 R 0.0189 0.7869 0.1941 62 D 0.0182 0.8453 0.1365 63 A 0.0223 0.8703 0.1075 64 V 0.0356 0.8604 0.1040 65 K 0.0285 0.8637 0.1078 66 L 0.0402 0.7860 0.1738 67 I 0.0875 0.5657 0.3468 68 R 0.0992 0.2473 0.6535 69 G 0.0540 0.1253 0.8206 70 S 0.1974 0.0534 0.7492 71 D 0.2886 0.0604 0.6511 72 V 0.6923 0.0301 0.2776 73 A 0.7276 0.0129 0.2595 74 I 0.8009 0.0069 0.1922 75 E 0.7913 0.0112 0.1975 76 F 0.7415 0.0305 0.2280 77 H 0.6087 0.0563 0.3351 78 T 0.3914 0.1475 0.4611 79 N 0.2305 0.1706 0.5989 80 A 0.1499 0.2913 0.5588 81 A 0.1665 0.2361 0.5974 82 A 0.1271 0.2636 0.6093 83 N 0.1412 0.1880 0.6708 84 K 0.1101 0.2867 0.6032 85 T 0.1792 0.1714 0.6495 86 A 0.2778 0.1237 0.5985 87 T 0.2882 0.0918 0.6200 88 G 0.4894 0.0435 0.4671 89 I 0.6839 0.0226 0.2935 90 E 0.7704 0.0154 0.2143 91 A 0.8024 0.0084 0.1892 92 L 0.7825 0.0117 0.2058 93 S 0.7166 0.0129 0.2705 94 T 0.4185 0.0216 0.5599 95 P 0.1971 0.1462 0.6567 96 K 0.0976 0.2795 0.6229 97 N 0.1029 0.2387 0.6584 98 K 0.0887 0.4142 0.4972 99 R 0.0584 0.5855 0.3561 100 W 0.0414 0.7085 0.2501 101 C 0.0212 0.8440 0.1348 102 Q 0.0098 0.9039 0.0863 103 V 0.0090 0.9139 0.0771 104 L 0.0086 0.9188 0.0726 105 G 0.0083 0.9214 0.0702 106 K 0.0083 0.9228 0.0689 107 A 0.0083 0.9227 0.0690 108 V 0.0084 0.9183 0.0733 109 A 0.0086 0.9105 0.0809 110 K 0.0093 0.8928 0.0980 111 K 0.0188 0.7611 0.2201 112 T 0.0668 0.4528 0.4804 113 G 0.0602 0.2832 0.6566 114 W 0.1351 0.2839 0.5810 115 K 0.2063 0.2062 0.5875 116 L 0.2381 0.1757 0.5862 117 R 0.2490 0.1381 0.6128 118 G 0.1695 0.1573 0.6732 119 E 0.1449 0.2650 0.5900 120 D 0.1223 0.1788 0.6989 121 G 0.1139 0.1057 0.7803 122 F 0.2584 0.0418 0.6998 123 K 0.2667 0.0289 0.7044 124 P 0.2161 0.1329 0.6510 125 D 0.1359 0.3210 0.5431 126 N 0.1293 0.2689 0.6019 127 A 0.1527 0.2469 0.6004 128 G 0.1709 0.2085 0.6207 129 Q 0.2179 0.1956 0.5865 130 H 0.4163 0.1290 0.4547 131 S 0.6115 0.0964 0.2921 132 R 0.7143 0.0622 0.2236 133 L 0.6630 0.0874 0.2497 134 A 0.5036 0.1699 0.3265 135 Y 0.3429 0.2083 0.4488 136 A 0.2262 0.2319 0.5419 137 Q 0.1984 0.1555 0.6461 138 A 0.2609 0.0967 0.6424 139 G 0.3075 0.1024 0.5902 140 G 0.5913 0.0629 0.3458 141 I 0.7380 0.0312 0.2309 142 V 0.7662 0.0216 0.2122 143 F 0.7439 0.0321 0.2241 144 E 0.6853 0.0346 0.2801 145 P 0.5321 0.1049 0.3631 146 F 0.4831 0.1128 0.4042 147 F 0.5129 0.1105 0.3765 148 I 0.3819 0.1144 0.5037 149 S 0.2400 0.0851 0.6750 150 N 0.1739 0.0516 0.7746 151 D 0.0214 0.6800 0.2985 152 T 0.0145 0.8033 0.1821 153 D 0.0159 0.8680 0.1161 154 L 0.0114 0.8915 0.0971 155 A 0.0108 0.8726 0.1166 156 L 0.0174 0.8045 0.1781 157 F 0.0303 0.7606 0.2090 158 K 0.0588 0.5173 0.4239 159 T 0.1072 0.3445 0.5482 160 T 0.0264 0.5248 0.4487 161 K 0.0220 0.6233 0.3547 162 W 0.0247 0.7323 0.2430 163 G 0.0225 0.7956 0.1819 164 I 0.0206 0.8619 0.1175 165 C 0.0109 0.9068 0.0823 166 R 0.0090 0.9189 0.0721 167 A 0.0094 0.9205 0.0701 168 I 0.0095 0.9166 0.0739 169 A 0.0144 0.8981 0.0874 170 D 0.0128 0.8698 0.1174 171 A 0.0402 0.8201 0.1397 172 I 0.1054 0.7101 0.1845 173 A 0.1350 0.5894 0.2756 174 M 0.1794 0.4866 0.3340 175 E 0.1828 0.3301 0.4871 176 L 0.1542 0.2120 0.6338 177 G 0.1302 0.0923 0.7776 178 A 0.1498 0.1948 0.6554 179 A 0.1723 0.1916 0.6360 180 K 0.2013 0.1741 0.6246 181 V 0.2261 0.1344 0.6395