# This file is the result of combining several RDB files, specifically # T0429.t04.str2.rdb (weight 1.54425) # T0429.t04.str4.rdb (weight 0.924988) # T0429.t04.pb.rdb (weight 0.789901) # T0429.t04.bys.rdb (weight 0.748322) # T0429.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 T0429.t04.str2.rdb # ============================================ # TARGET T0429 # 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 T0429.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 7.37887 # # ============================================ # Comments from T0429.t04.str4.rdb # ============================================ # TARGET T0429 # 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 T0429.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 7.37887 # # ============================================ # Comments from T0429.t04.pb.rdb # ============================================ # TARGET T0429 # 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 T0429.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 7.37887 # # ============================================ # Comments from T0429.t04.bys.rdb # ============================================ # TARGET T0429 # 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 T0429.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 7.37887 # # ============================================ # Comments from T0429.t04.alpha.rdb # ============================================ # TARGET T0429 # 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 T0429.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 7.37887 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 R 0.2477 0.1042 0.6481 2 V 0.2905 0.1045 0.6050 3 T 0.2597 0.1282 0.6121 4 R 0.2458 0.2003 0.5540 5 K 0.2288 0.1288 0.6424 6 A 0.2717 0.0615 0.6668 7 P 0.2290 0.1195 0.6515 8 S 0.2337 0.1705 0.5958 9 R 0.1900 0.2085 0.6015 10 D 0.2031 0.1362 0.6607 11 E 0.3020 0.0552 0.6428 12 P 0.3069 0.0797 0.6135 13 C 0.3378 0.1018 0.5604 14 S 0.2796 0.1222 0.5982 15 S 0.2493 0.1868 0.5638 16 T 0.2129 0.1631 0.6240 17 S 0.1966 0.1255 0.6779 18 R 0.2452 0.0668 0.6880 19 P 0.2153 0.1462 0.6385 20 A 0.2311 0.1666 0.6023 21 L 0.2125 0.1797 0.6078 22 E 0.1885 0.2676 0.5438 23 E 0.2014 0.2837 0.5149 24 D 0.3626 0.1321 0.5053 25 V 0.6364 0.0302 0.3334 26 I 0.7297 0.0174 0.2529 27 Y 0.7979 0.0084 0.1937 28 H 0.8105 0.0062 0.1833 29 V 0.8067 0.0058 0.1876 30 K 0.7373 0.0104 0.2524 31 Y 0.6063 0.0374 0.3563 32 D 0.2995 0.1678 0.5327 33 D 0.1766 0.1527 0.6707 34 Y 0.2665 0.0536 0.6800 35 P 0.1417 0.2408 0.6175 36 E 0.0921 0.3397 0.5682 37 N 0.1462 0.1549 0.6989 38 G 0.3086 0.0693 0.6220 39 V 0.5977 0.0315 0.3708 40 V 0.7201 0.0208 0.2591 41 Q 0.7542 0.0112 0.2346 42 M 0.7114 0.0210 0.2676 43 N 0.4808 0.0311 0.4880 44 S 0.2401 0.2637 0.4962 45 R 0.1342 0.3337 0.5321 46 D 0.2103 0.1916 0.5981 47 V 0.2898 0.1062 0.6040 48 R 0.2492 0.1022 0.6486 49 A 0.1673 0.4669 0.3658 50 R 0.1502 0.4889 0.3610 51 A 0.1687 0.5624 0.2688 52 R 0.2437 0.4660 0.2903 53 T 0.4656 0.2708 0.2636 54 I 0.5046 0.1724 0.3230 55 I 0.4860 0.1024 0.4116 56 K 0.3270 0.0793 0.5938 57 W 0.1615 0.3879 0.4506 58 Q 0.1263 0.4246 0.4491 59 D 0.2204 0.2859 0.4937 60 L 0.4018 0.0845 0.5137 61 E 0.3766 0.0805 0.5429 62 V 0.2826 0.0975 0.6198 63 G 0.2390 0.0656 0.6955 64 Q 0.5166 0.0217 0.4617 65 V 0.7406 0.0072 0.2522 66 V 0.7783 0.0099 0.2118 67 M 0.7864 0.0085 0.2051 68 L 0.7609 0.0182 0.2210 69 N 0.6303 0.0197 0.3500 70 Y 0.3647 0.0564 0.5789 71 N 0.2332 0.0242 0.7425 72 P 0.0409 0.3936 0.5654 73 D 0.0731 0.2578 0.6691 74 N 0.2055 0.1048 0.6897 75 P 0.1436 0.2549 0.6015 76 K 0.1231 0.3740 0.5029 77 E 0.1820 0.2383 0.5797 78 R 0.2168 0.1325 0.6508 79 G 0.2547 0.0796 0.6656 80 F 0.5134 0.0586 0.4281 81 W 0.6430 0.0545 0.3025 82 Y 0.6851 0.0549 0.2600 83 D 0.6503 0.0694 0.2804 84 A 0.6309 0.1120 0.2570 85 E 0.6245 0.1593 0.2161 86 I 0.5631 0.1743 0.2625 87 S 0.4411 0.2296 0.3293 88 R 0.3530 0.3001 0.3469 89 K 0.3018 0.2853 0.4128 90 R 0.2760 0.2906 0.4334 91 E 0.2856 0.2406 0.4738 92 T 0.2796 0.1778 0.5426 93 R 0.2850 0.2051 0.5099 94 T 0.3039 0.1772 0.5189 95 A 0.2179 0.3603 0.4218 96 R 0.2557 0.3767 0.3676 97 E 0.4458 0.2597 0.2945 98 L 0.5508 0.1582 0.2909 99 Y 0.5905 0.0931 0.3165 100 A 0.4620 0.0989 0.4391 101 N 0.2389 0.1066 0.6545