# This file is the result of combining several RDB files, specifically # T0460.t04.str2.rdb (weight 1.54425) # T0460.t04.str4.rdb (weight 0.924988) # T0460.t04.pb.rdb (weight 0.789901) # T0460.t04.bys.rdb (weight 0.748322) # T0460.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 T0460.t04.str2.rdb # ============================================ # TARGET T0460 # 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 T0460.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 2.18387 # # ============================================ # Comments from T0460.t04.str4.rdb # ============================================ # TARGET T0460 # 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 T0460.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 2.18387 # # ============================================ # Comments from T0460.t04.pb.rdb # ============================================ # TARGET T0460 # 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 T0460.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 2.18387 # # ============================================ # Comments from T0460.t04.bys.rdb # ============================================ # TARGET T0460 # 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 T0460.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 2.18387 # # ============================================ # Comments from T0460.t04.alpha.rdb # ============================================ # TARGET T0460 # 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 T0460.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 2.18387 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.1719 0.2344 0.5937 2 N 0.1445 0.3011 0.5545 3 S 0.0233 0.7308 0.2459 4 E 0.0164 0.8451 0.1385 5 V 0.0232 0.8807 0.0961 6 I 0.0121 0.9007 0.0871 7 K 0.0095 0.9129 0.0776 8 E 0.0087 0.9101 0.0812 9 F 0.0100 0.8898 0.1002 10 L 0.0116 0.8495 0.1389 11 E 0.0108 0.8482 0.1409 12 D 0.0292 0.7104 0.2604 13 I 0.0690 0.4234 0.5076 14 G 0.0650 0.2941 0.6409 15 E 0.0820 0.4451 0.4729 16 D 0.1261 0.3672 0.5067 17 Y 0.2913 0.3237 0.3849 18 I 0.5124 0.1971 0.2906 19 E 0.6181 0.0996 0.2823 20 L 0.5306 0.1179 0.3515 21 E 0.2994 0.1642 0.5364 22 N 0.1874 0.1208 0.6918 23 E 0.3676 0.0869 0.5455 24 I 0.5461 0.0504 0.4034 25 H 0.5547 0.0417 0.4036 26 L 0.5138 0.0466 0.4396 27 K 0.3563 0.0329 0.6108 28 P 0.2724 0.2226 0.5050 29 E 0.2786 0.3516 0.3699 30 V 0.4562 0.2804 0.2634 31 F 0.4329 0.3591 0.2079 32 Y 0.4853 0.3536 0.1612 33 E 0.4455 0.4132 0.1413 34 V 0.4174 0.4335 0.1491 35 W 0.3656 0.4459 0.1885 36 K 0.3111 0.4467 0.2422 37 Y 0.2636 0.3778 0.3586 38 V 0.1932 0.1931 0.6137 39 G 0.1348 0.1088 0.7564 40 E 0.2199 0.0686 0.7115 41 P 0.2048 0.2147 0.5804 42 E 0.2515 0.2304 0.5181 43 L 0.3953 0.1655 0.4392 44 K 0.4925 0.1193 0.3883 45 T 0.6956 0.0309 0.2735 46 Y 0.7312 0.0163 0.2525 47 V 0.7646 0.0110 0.2244 48 I 0.6964 0.0259 0.2777 49 E 0.5386 0.0913 0.3701 50 D 0.3452 0.1306 0.5242 51 E 0.3774 0.1185 0.5042 52 I 0.4396 0.0934 0.4670 53 V 0.4287 0.0662 0.5051 54 E 0.3292 0.0425 0.6283 55 P 0.1990 0.1422 0.6589 56 G 0.1543 0.1449 0.7008 57 E 0.2608 0.1335 0.6057 58 Y 0.3425 0.0863 0.5712 59 D 0.2492 0.0372 0.7135 60 P 0.1384 0.1995 0.6620 61 P 0.0603 0.4743 0.4654 62 E 0.0917 0.4265 0.4818 63 M 0.2697 0.2519 0.4785 64 K 0.3508 0.1856 0.4636 65 Y 0.4154 0.1458 0.4389 66 T 0.3213 0.1544 0.5243 67 N 0.3146 0.1253 0.5601 68 V 0.4358 0.0867 0.4775 69 K 0.4882 0.1155 0.3963 70 K 0.6967 0.0316 0.2717 71 V 0.6777 0.0183 0.3041 72 K 0.7046 0.0152 0.2802 73 I 0.6693 0.0150 0.3157 74 K 0.6010 0.0475 0.3516 75 K 0.7391 0.0162 0.2447 76 V 0.7251 0.0145 0.2603 77 Y 0.7451 0.0193 0.2357 78 F 0.7397 0.0247 0.2356 79 E 0.6907 0.0515 0.2579 80 T 0.5842 0.0619 0.3539 81 L 0.3956 0.1321 0.4723 82 D 0.2072 0.1330 0.6598 83 N 0.1324 0.0991 0.7684 84 V 0.3730 0.0340 0.5930 85 R 0.5898 0.0288 0.3814 86 V 0.7198 0.0244 0.2558 87 V 0.6290 0.0492 0.3218 88 T 0.4593 0.0600 0.4807 89 D 0.2488 0.0879 0.6634 90 Y 0.0511 0.5426 0.4063 91 S 0.0199 0.7434 0.2367 92 E 0.0102 0.8787 0.1111 93 F 0.0100 0.9050 0.0850 94 Q 0.0086 0.9206 0.0708 95 K 0.0086 0.9204 0.0710 96 I 0.0094 0.9181 0.0725 97 L 0.0119 0.9044 0.0837 98 K 0.0121 0.8850 0.1030 99 K 0.0212 0.7800 0.1988 100 R 0.0617 0.3791 0.5591 101 G 0.0578 0.1587 0.7836 102 T 0.1723 0.1464 0.6812 103 K 0.2826 0.1756 0.5418 104 L 0.3149 0.2440 0.4411 105 E 0.2575 0.3043 0.4382 106 H 0.2561 0.2838 0.4602 107 H 0.2156 0.2477 0.5367 108 H 0.2085 0.2242 0.5673 109 H 0.2055 0.1965 0.5980 110 H 0.1968 0.1700 0.6332 111 H 0.2059 0.1366 0.6575