# This file is the result of combining several RDB files, specifically # T0514.t2k.str2.rdb (weight 1.54425) # T0514.t2k.str4.rdb (weight 0.924988) # T0514.t2k.pb.rdb (weight 0.789901) # T0514.t2k.bys.rdb (weight 0.748322) # T0514.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 T0514.t2k.str2.rdb # ============================================ # TARGET T0514 # 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 T0514.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 70.296 # # ============================================ # Comments from T0514.t2k.str4.rdb # ============================================ # TARGET T0514 # 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 T0514.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 70.296 # # ============================================ # Comments from T0514.t2k.pb.rdb # ============================================ # TARGET T0514 # 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 T0514.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 70.296 # # ============================================ # Comments from T0514.t2k.bys.rdb # ============================================ # TARGET T0514 # 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 T0514.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 70.296 # # ============================================ # Comments from T0514.t2k.alpha.rdb # ============================================ # TARGET T0514 # 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 T0514.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 70.296 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 S 0.2483 0.1777 0.5740 2 S 0.3254 0.1316 0.5430 3 L 0.3940 0.1836 0.4224 4 T 0.4079 0.1880 0.4041 5 E 0.4299 0.1858 0.3843 6 T 0.3656 0.1879 0.4465 7 Y 0.3025 0.0995 0.5980 8 G 0.2142 0.0868 0.6990 9 L 0.3520 0.0914 0.5566 10 W 0.5831 0.0647 0.3522 11 S 0.6899 0.0358 0.2744 12 I 0.7319 0.0278 0.2403 13 N 0.6978 0.0316 0.2706 14 C 0.6167 0.0524 0.3309 15 G 0.4903 0.0710 0.4387 16 I 0.4041 0.0888 0.5071 17 Q 0.2843 0.1403 0.5753 18 E 0.1339 0.1752 0.6909 19 G 0.0697 0.1332 0.7971 20 K 0.2158 0.0919 0.6923 21 K 0.3883 0.0802 0.5315 22 V 0.5485 0.0836 0.3679 23 C 0.6239 0.0812 0.2949 24 F 0.6783 0.0880 0.2337 25 M 0.6561 0.1112 0.2327 26 H 0.6298 0.1286 0.2416 27 R 0.6299 0.1190 0.2512 28 Q 0.6401 0.1118 0.2481 29 E 0.6178 0.1027 0.2795 30 V 0.5174 0.1242 0.3583 31 N 0.2623 0.1648 0.5729 32 D 0.1359 0.2397 0.6244 33 Q 0.0914 0.1859 0.7227 34 N 0.0833 0.1173 0.7994 35 R 0.3730 0.0206 0.6064 36 V 0.6455 0.0122 0.3423 37 V 0.7665 0.0099 0.2236 38 V 0.8011 0.0091 0.1898 39 A 0.8114 0.0069 0.1817 40 M 0.8105 0.0080 0.1815 41 S 0.8105 0.0081 0.1814 42 V 0.7950 0.0125 0.1925 43 V 0.7573 0.0137 0.2290 44 L 0.6769 0.0166 0.3065 45 N 0.4387 0.0264 0.5349 46 A 0.1415 0.2698 0.5887 47 D 0.0595 0.1745 0.7660 48 G 0.1149 0.0809 0.8041 49 V 0.4633 0.0185 0.5182 50 V 0.6171 0.0171 0.3658 51 S 0.6862 0.0171 0.2966 52 G 0.7739 0.0085 0.2176 53 N 0.7935 0.0064 0.2001 54 L 0.8152 0.0056 0.1792 55 T 0.7873 0.0070 0.2057 56 V 0.6994 0.0110 0.2896 57 P 0.5502 0.0296 0.4202 58 F 0.3233 0.1194 0.5573 59 G 0.2965 0.1196 0.5839 60 I 0.4957 0.0849 0.4195 61 L 0.5554 0.0639 0.3807 62 V 0.4892 0.0477 0.4631 63 S 0.3433 0.0522 0.6045 64 K 0.3094 0.0841 0.6066 65 P 0.3443 0.0585 0.5972 66 V 0.5285 0.0197 0.4519 67 R 0.7386 0.0103 0.2511 68 L 0.7910 0.0071 0.2019 69 Q 0.7702 0.0077 0.2221 70 V 0.6499 0.0241 0.3259 71 D 0.3227 0.0419 0.6354 72 E 0.1295 0.1879 0.6827 73 G 0.1154 0.1443 0.7403 74 K 0.3004 0.1196 0.5800 75 A 0.3979 0.1306 0.4715 76 V 0.4481 0.1430 0.4088 77 I 0.4448 0.1748 0.3804 78 E 0.3989 0.1475 0.4536 79 T 0.3435 0.1027 0.5538 80 G 0.3478 0.0947 0.5574 81 I 0.4808 0.0987 0.4205 82 R 0.5613 0.0752 0.3635 83 T 0.6081 0.0568 0.3351 84 C 0.5457 0.0497 0.4045 85 V 0.4365 0.0356 0.5279 86 P 0.3375 0.0995 0.5630 87 A 0.2029 0.1268 0.6703 88 G 0.2206 0.0789 0.7005 89 C 0.4252 0.0326 0.5422 90 I 0.6749 0.0285 0.2966 91 V 0.6942 0.0175 0.2883 92 P 0.6695 0.0200 0.3105 93 I 0.6369 0.0295 0.3335 94 V 0.4673 0.0445 0.4881 95 F 0.3278 0.0575 0.6148 96 D 0.1631 0.0647 0.7722 97 K 0.0112 0.7475 0.2414 98 N 0.0094 0.8665 0.1241 99 Y 0.0086 0.9189 0.0725 100 V 0.0083 0.9210 0.0707 101 A 0.0083 0.9239 0.0678 102 A 0.0084 0.9192 0.0725 103 L 0.0088 0.9021 0.0892 104 R 0.0124 0.8192 0.1684 105 A 0.0339 0.4965 0.4696 106 G 0.0549 0.1795 0.7656 107 K 0.1326 0.1892 0.6782 108 H 0.3455 0.0796 0.5749 109 L 0.6086 0.0210 0.3704 110 K 0.7523 0.0094 0.2383 111 L 0.8021 0.0070 0.1909 112 A 0.7914 0.0090 0.1997 113 M 0.7926 0.0080 0.1994 114 T 0.7544 0.0091 0.2365 115 I 0.6133 0.0219 0.3648 116 A 0.4331 0.0558 0.5111 117 A 0.2962 0.0556 0.6483 118 P 0.1596 0.1076 0.7327 119 G 0.1284 0.0838 0.7878 120 E 0.1747 0.0564 0.7689 121 P 0.1921 0.0849 0.7230 122 P 0.2288 0.0968 0.6744 123 L 0.3225 0.1215 0.5560 124 N 0.4262 0.0588 0.5149 125 D 0.5496 0.0381 0.4122 126 L 0.6199 0.0235 0.3566 127 F 0.6784 0.0186 0.3030 128 V 0.6543 0.0241 0.3216 129 Q 0.4800 0.0490 0.4710 130 L 0.2994 0.2488 0.4517 131 N 0.1336 0.2764 0.5901 132 G 0.0774 0.2557 0.6669 133 F 0.0616 0.6137 0.3247 134 S 0.0178 0.8270 0.1552 135 N 0.0094 0.8941 0.0965 136 A 0.0086 0.9075 0.0838 137 L 0.0086 0.9110 0.0804 138 N 0.0085 0.9080 0.0835 139 R 0.0094 0.8927 0.0980 140 L 0.0102 0.8893 0.1005 141 I 0.0094 0.8947 0.0959 142 A 0.0118 0.8667 0.1215 143 L 0.0285 0.7749 0.1966 144 Q 0.0660 0.6222 0.3118 145 K 0.0732 0.4758 0.4510