# This file is the result of combining several RDB files, specifically # T0487.t2k.str2.rdb (weight 1.54425) # T0487.t2k.str4.rdb (weight 0.924988) # T0487.t2k.pb.rdb (weight 0.789901) # T0487.t2k.bys.rdb (weight 0.748322) # T0487.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 T0487.t2k.str2.rdb # ============================================ # TARGET T0487 # 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 T0487.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 4.34599 # # ============================================ # Comments from T0487.t2k.str4.rdb # ============================================ # TARGET T0487 # 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 T0487.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 4.34599 # # ============================================ # Comments from T0487.t2k.pb.rdb # ============================================ # TARGET T0487 # 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 T0487.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 4.34599 # # ============================================ # Comments from T0487.t2k.bys.rdb # ============================================ # TARGET T0487 # 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 T0487.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 4.34599 # # ============================================ # Comments from T0487.t2k.alpha.rdb # ============================================ # TARGET T0487 # 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 T0487.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 4.34599 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 G 0.0858 0.0869 0.8273 2 R 0.2191 0.0950 0.6859 3 R 0.3460 0.0759 0.5781 4 A 0.4058 0.1012 0.4930 5 V 0.3561 0.1236 0.5202 6 S 0.2403 0.1280 0.6317 7 K 0.3207 0.0780 0.6013 8 P 0.2698 0.1755 0.5546 9 A 0.2674 0.3493 0.3833 10 D 0.2505 0.4021 0.3474 11 A 0.2166 0.4826 0.3008 12 L 0.2077 0.4552 0.3370 13 R 0.2676 0.3130 0.4194 14 V 0.2185 0.2169 0.5646 15 G 0.1980 0.1375 0.6645 16 F 0.4106 0.1342 0.4552 17 Y 0.5222 0.1156 0.3622 18 R 0.5093 0.1238 0.3669 19 A 0.3160 0.2810 0.4030 20 Q 0.2886 0.2399 0.4715 21 E 0.4116 0.2075 0.3809 22 T 0.5294 0.1558 0.3149 23 A 0.5408 0.1618 0.2974 24 L 0.6487 0.1027 0.2486 25 A 0.6940 0.0775 0.2285 26 L 0.7120 0.0534 0.2347 27 L 0.7505 0.0253 0.2242 28 R 0.5866 0.0313 0.3821 29 L 0.3262 0.1152 0.5586 30 D 0.1299 0.1347 0.7354 31 G 0.0647 0.1031 0.8322 32 A 0.1470 0.1665 0.6865 33 Q 0.1513 0.1930 0.6556 34 G 0.1303 0.1572 0.7124 35 W 0.1550 0.0976 0.7473 36 P 0.0636 0.6223 0.3142 37 E 0.0110 0.8339 0.1552 38 F 0.0088 0.9018 0.0894 39 L 0.0083 0.9210 0.0706 40 R 0.0083 0.9235 0.0682 41 R 0.0083 0.9241 0.0676 42 A 0.0083 0.9247 0.0670 43 L 0.0083 0.9227 0.0690 44 L 0.0083 0.9222 0.0695 45 R 0.0084 0.9196 0.0721 46 A 0.0106 0.8613 0.1280 47 F 0.0286 0.6969 0.2746 48 G 0.0389 0.5086 0.4525 49 A 0.0581 0.5431 0.3989 50 S 0.0643 0.1576 0.7781 51 G 0.0696 0.0766 0.8538 52 A 0.3073 0.0265 0.6662 53 S 0.6120 0.0202 0.3677 54 L 0.7369 0.0119 0.2512 55 R 0.7354 0.0120 0.2526 56 L 0.6777 0.0337 0.2887 57 H 0.5685 0.0678 0.3637 58 T 0.4465 0.1344 0.4191 59 L 0.3161 0.1978 0.4861 60 H 0.2521 0.2034 0.5445 61 A 0.2280 0.1435 0.6285 62 H 0.2221 0.0612 0.7168 63 P 0.1285 0.1854 0.6861 64 S 0.0751 0.3876 0.5374 65 Q 0.0726 0.3391 0.5883 66 G 0.0637 0.3758 0.5605 67 L 0.0791 0.6273 0.2936 68 A 0.0543 0.7552 0.1905 69 F 0.0281 0.8516 0.1203 70 R 0.0104 0.9091 0.0804 71 E 0.0085 0.9203 0.0712 72 A 0.0088 0.9186 0.0726 73 L 0.0088 0.9197 0.0715 74 R 0.0089 0.9184 0.0727 75 K 0.0104 0.9098 0.0797 76 A 0.0136 0.8945 0.0919 77 K 0.0135 0.8669 0.1196 78 E 0.0220 0.7797 0.1982 79 E 0.0550 0.2560 0.6889 80 G 0.0492 0.0683 0.8825 81 V 0.2601 0.0217 0.7182 82 Q 0.4080 0.0304 0.5616 83 A 0.7778 0.0085 0.2136 84 V 0.7898 0.0057 0.2045 85 L 0.7909 0.0046 0.2044 86 V 0.8135 0.0045 0.1820 87 L 0.7602 0.0106 0.2292 88 T 0.4484 0.0140 0.5376 89 P 0.2458 0.0652 0.6890 90 P 0.1865 0.1490 0.6645 91 M 0.1943 0.1315 0.6742 92 A 0.1281 0.3552 0.5167 93 W 0.0806 0.5354 0.3840 94 E 0.0599 0.6288 0.3113 95 D 0.0596 0.6317 0.3087 96 R 0.0390 0.7512 0.2098 97 N 0.0301 0.7945 0.1754 98 R 0.0468 0.7940 0.1592 99 L 0.0545 0.8205 0.1250 100 K 0.0295 0.8759 0.0946 101 A 0.0150 0.9051 0.0799 102 L 0.0106 0.9131 0.0763 103 L 0.0115 0.9045 0.0840 104 L 0.0126 0.8779 0.1095 105 R 0.0203 0.7766 0.2031 106 E 0.0523 0.3215 0.6262 107 G 0.0458 0.0925 0.8616 108 L 0.1674 0.0545 0.7781 109 P 0.1658 0.2565 0.5777 110 S 0.2003 0.3531 0.4466 111 Q 0.3098 0.3021 0.3881 112 I 0.4242 0.2141 0.3617 113 L 0.4963 0.1072 0.3965 114 N 0.4268 0.0757 0.4975 115 V 0.4009 0.0212 0.5779 116 P 0.3452 0.0220 0.6328 117 L 0.2874 0.0538 0.6588 118 R 0.1669 0.1397 0.6933 119 E 0.0782 0.4372 0.4847 120 E 0.0726 0.5160 0.4115 121 E 0.1048 0.4641 0.4311 122 R 0.1027 0.5362 0.3611 123 H 0.1175 0.5379 0.3446 124 R 0.0871 0.6245 0.2884 125 W 0.0461 0.7889 0.1650 126 E 0.0224 0.8496 0.1281 127 N 0.0224 0.8608 0.1168 128 A 0.0217 0.8828 0.0955 129 L 0.0173 0.8879 0.0947 130 L 0.0133 0.9005 0.0862 131 G 0.0109 0.9093 0.0798 132 L 0.0104 0.9121 0.0775 133 L 0.0125 0.9009 0.0867 134 A 0.0145 0.8704 0.1151 135 K 0.0280 0.7657 0.2063 136 A 0.0628 0.4354 0.5018 137 G 0.0684 0.1797 0.7519 138 L 0.1714 0.1339 0.6947 139 Q 0.3122 0.0613 0.6265 140 V 0.3996 0.0753 0.5251 141 V 0.3566 0.0756 0.5678