# This file is the result of combining several RDB files, specifically # T0411.t06.str2.rdb (weight 1.54425) # T0411.t06.str4.rdb (weight 0.924988) # T0411.t06.pb.rdb (weight 0.789901) # T0411.t06.bys.rdb (weight 0.748322) # T0411.t06.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 T0411.t06.str2.rdb # ============================================ # TARGET T0411 # Using neural net dunbrack-40pc-3157-t06-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 T0411.t06-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 1713 # # ============================================ # Comments from T0411.t06.str4.rdb # ============================================ # TARGET T0411 # Using neural net dunbrack-40pc-3157-t06-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 T0411.t06-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 1713 # # ============================================ # Comments from T0411.t06.pb.rdb # ============================================ # TARGET T0411 # Using neural net dunbrack-40pc-3157-t06-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 T0411.t06-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 1713 # # ============================================ # Comments from T0411.t06.bys.rdb # ============================================ # TARGET T0411 # Using neural net dunbrack-40pc-3157-t06-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 T0411.t06-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 1713 # # ============================================ # Comments from T0411.t06.alpha.rdb # ============================================ # TARGET T0411 # Using neural net dunbrack-40pc-3157-t06-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 T0411.t06-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 1713 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.2434 0.2253 0.5313 2 W 0.2191 0.3175 0.4634 3 K 0.2010 0.4351 0.3639 4 A 0.2518 0.4276 0.3206 5 V 0.2899 0.3945 0.3156 6 M 0.3210 0.3369 0.3421 7 N 0.2722 0.3108 0.4171 8 A 0.1912 0.3137 0.4951 9 W 0.1492 0.3053 0.5455 10 N 0.1249 0.2033 0.6719 11 G 0.1222 0.1217 0.7560 12 T 0.1821 0.1323 0.6856 13 E 0.1456 0.3025 0.5519 14 S 0.1893 0.2790 0.5316 15 Q 0.2238 0.2130 0.5632 16 S 0.2197 0.1586 0.6217 17 K 0.1568 0.2919 0.5513 18 N 0.1704 0.2174 0.6122 19 V 0.1862 0.1881 0.6257 20 S 0.1607 0.2095 0.6297 21 N 0.1529 0.1863 0.6608 22 I 0.2394 0.1278 0.6328 23 Q 0.3598 0.1051 0.5352 24 S 0.4422 0.0553 0.5025 25 Y 0.4346 0.0272 0.5382 26 S 0.2007 0.0143 0.7850 27 F 0.0186 0.7215 0.2599 28 E 0.0100 0.8609 0.1291 29 D 0.0098 0.9122 0.0780 30 M 0.0085 0.9204 0.0711 31 K 0.0084 0.9163 0.0753 32 R 0.0084 0.9121 0.0794 33 I 0.0104 0.8643 0.1253 34 V 0.0232 0.7392 0.2377 35 G 0.0267 0.4632 0.5101 36 K 0.0648 0.3210 0.6142 37 H 0.1057 0.1751 0.7192 38 D 0.1818 0.0491 0.7691 39 P 0.0804 0.3555 0.5641 40 N 0.1478 0.1393 0.7129 41 V 0.6287 0.0134 0.3578 42 V 0.7186 0.0146 0.2668 43 L 0.7625 0.0070 0.2306 44 V 0.7676 0.0129 0.2195 45 D 0.6668 0.0141 0.3191 46 V 0.4580 0.0664 0.4756 47 R 0.3048 0.0492 0.6459 48 E 0.2014 0.0230 0.7757 49 P 0.0778 0.4015 0.5207 50 S 0.0601 0.5347 0.4052 51 E 0.1327 0.4668 0.4004 52 Y 0.2538 0.2940 0.4521 53 S 0.2896 0.2387 0.4717 54 I 0.3468 0.1895 0.4637 55 V 0.4010 0.1124 0.4866 56 H 0.4217 0.0674 0.5110 57 I 0.3170 0.0428 0.6402 58 P 0.1896 0.1385 0.6719 59 A 0.1516 0.1618 0.6866 60 S 0.2932 0.1561 0.5507 61 I 0.4446 0.0926 0.4629 62 N 0.4204 0.0684 0.5112 63 V 0.3739 0.0400 0.5861 64 P 0.2445 0.0703 0.6852 65 Y 0.1461 0.3386 0.5154 66 R 0.1017 0.3872 0.5111 67 S 0.1454 0.2942 0.5604 68 H 0.2084 0.0993 0.6923 69 P 0.0908 0.3561 0.5531 70 D 0.0912 0.3007 0.6082 71 A 0.0854 0.3809 0.5337 72 F 0.1252 0.3272 0.5477 73 A 0.1710 0.2250 0.6040 74 L 0.2145 0.0901 0.6954 75 D 0.1709 0.0247 0.8045 76 P 0.0138 0.7303 0.2559 77 L 0.0095 0.8543 0.1362 78 E 0.0095 0.9102 0.0803 79 F 0.0097 0.9145 0.0758 80 E 0.0087 0.9052 0.0860 81 K 0.0089 0.8993 0.0918 82 Q 0.0140 0.8149 0.1711 83 I 0.0519 0.5485 0.3997 84 G 0.0461 0.2853 0.6686 85 I 0.1487 0.1441 0.7072 86 P 0.1493 0.1250 0.7257 87 K 0.1932 0.0656 0.7412 88 P 0.1678 0.0998 0.7324 89 D 0.1631 0.0772 0.7597 90 S 0.0479 0.3965 0.5556 91 A 0.0884 0.2035 0.7081 92 K 0.3089 0.0550 0.6361 93 E 0.5727 0.0205 0.4068 94 L 0.7784 0.0078 0.2138 95 I 0.8113 0.0057 0.1830 96 F 0.8083 0.0061 0.1856 97 Y 0.7742 0.0088 0.2169 98 C 0.5322 0.0229 0.4449 99 A 0.2460 0.1694 0.5845 100 S 0.1345 0.1789 0.6866 101 G 0.0970 0.1939 0.7091 102 K 0.1256 0.3963 0.4780 103 R 0.0918 0.5782 0.3300 104 G 0.0300 0.7931 0.1769 105 G 0.0097 0.8916 0.0987 106 E 0.0085 0.9164 0.0752 107 A 0.0083 0.9224 0.0693 108 Q 0.0083 0.9225 0.0692 109 K 0.0083 0.9242 0.0675 110 V 0.0083 0.9233 0.0684 111 A 0.0084 0.9195 0.0721 112 S 0.0088 0.9041 0.0871 113 S 0.0152 0.7695 0.2153 114 H 0.0578 0.2447 0.6975 115 G 0.0510 0.0795 0.8695 116 Y 0.1712 0.0533 0.7755 117 S 0.1584 0.2052 0.6363 118 N 0.2181 0.1193 0.6626 119 T 0.5334 0.0428 0.4238 120 S 0.6893 0.0283 0.2824 121 L 0.6926 0.0238 0.2836 122 Y 0.5448 0.0234 0.4318 123 P 0.2227 0.1285 0.6489 124 G 0.1081 0.1384 0.7535 125 S 0.1725 0.1737 0.6538 126 M 0.0686 0.6250 0.3064 127 N 0.0421 0.7420 0.2158 128 D 0.0364 0.8108 0.1528 129 W 0.0387 0.8125 0.1488 130 V 0.0496 0.7813 0.1691 131 S 0.0610 0.6238 0.3152 132 H 0.0804 0.3606 0.5590 133 G 0.0773 0.1551 0.7675 134 G 0.1283 0.1031 0.7686 135 D 0.1533 0.1143 0.7324 136 K 0.1697 0.1384 0.6920 137 L 0.2293 0.1295 0.6412 138 D 0.2447 0.0978 0.6575 139 L 0.1993 0.2001 0.6006