# 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) # T0411.t04.str2.rdb (weight 1.54425) # T0411.t04.str4.rdb (weight 0.924988) # T0411.t04.pb.rdb (weight 0.789901) # T0411.t04.bys.rdb (weight 0.748322) # T0411.t04.alpha.rdb (weight 0.678173) # T0411.t2k.str2.rdb (weight 1.54425) # T0411.t2k.str4.rdb (weight 0.924988) # T0411.t2k.pb.rdb (weight 0.789901) # T0411.t2k.bys.rdb (weight 0.748322) # T0411.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 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 # # ============================================ # Comments from T0411.t04.str2.rdb # ============================================ # TARGET T0411 # 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 T0411.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 2643 # # ============================================ # Comments from T0411.t04.str4.rdb # ============================================ # TARGET T0411 # 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 T0411.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 2643 # # ============================================ # Comments from T0411.t04.pb.rdb # ============================================ # TARGET T0411 # 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 T0411.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 2643 # # ============================================ # Comments from T0411.t04.bys.rdb # ============================================ # TARGET T0411 # 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 T0411.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 2643 # # ============================================ # Comments from T0411.t04.alpha.rdb # ============================================ # TARGET T0411 # 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 T0411.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 2643 # # ============================================ # Comments from T0411.t2k.str2.rdb # ============================================ # TARGET T0411 # 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 T0411.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 2801 # # ============================================ # Comments from T0411.t2k.str4.rdb # ============================================ # TARGET T0411 # 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 T0411.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 2801 # # ============================================ # Comments from T0411.t2k.pb.rdb # ============================================ # TARGET T0411 # 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 T0411.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 2801 # # ============================================ # Comments from T0411.t2k.bys.rdb # ============================================ # TARGET T0411 # 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 T0411.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 2801 # # ============================================ # Comments from T0411.t2k.alpha.rdb # ============================================ # TARGET T0411 # 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 T0411.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 2801 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.2212 0.2924 0.4863 2 W 0.2476 0.2845 0.4680 3 K 0.3884 0.3076 0.3040 4 A 0.5402 0.2773 0.1825 5 V 0.5474 0.2977 0.1549 6 M 0.5168 0.3223 0.1609 7 N 0.4927 0.3296 0.1777 8 A 0.4340 0.3182 0.2478 9 W 0.3543 0.2733 0.3724 10 N 0.2857 0.2256 0.4888 11 G 0.2659 0.2112 0.5228 12 T 0.2742 0.2321 0.4937 13 E 0.2720 0.2472 0.4808 14 S 0.2447 0.2702 0.4851 15 Q 0.2395 0.2595 0.5010 16 S 0.2525 0.2225 0.5250 17 K 0.2760 0.1774 0.5466 18 N 0.2844 0.1085 0.6071 19 V 0.2512 0.2356 0.5132 20 S 0.2191 0.2491 0.5318 21 N 0.2060 0.2338 0.5602 22 I 0.2124 0.1782 0.6094 23 Q 0.1994 0.1865 0.6141 24 S 0.2432 0.1680 0.5888 25 Y 0.3261 0.1127 0.5613 26 S 0.3491 0.0950 0.5560 27 F 0.3002 0.1114 0.5885 28 E 0.1726 0.1911 0.6363 29 D 0.0264 0.7481 0.2255 30 M 0.0126 0.8637 0.1237 31 K 0.0123 0.9047 0.0830 32 R 0.0109 0.9109 0.0782 33 I 0.0146 0.8897 0.0957 34 V 0.0273 0.7838 0.1889 35 G 0.0467 0.5463 0.4070 36 K 0.0817 0.3560 0.5623 37 H 0.1003 0.1812 0.7185 38 D 0.1980 0.0489 0.7531 39 P 0.1194 0.2440 0.6366 40 N 0.1522 0.1099 0.7379 41 V 0.5419 0.0132 0.4449 42 V 0.7073 0.0145 0.2782 43 L 0.7819 0.0056 0.2125 44 V 0.7847 0.0090 0.2063 45 D 0.6817 0.0077 0.3105 46 V 0.4219 0.0834 0.4948 47 R 0.3089 0.0591 0.6320 48 E 0.1971 0.0245 0.7784 49 P 0.0946 0.3779 0.5275 50 S 0.0599 0.5492 0.3909 51 E 0.1170 0.4861 0.3969 52 Y 0.2283 0.3462 0.4255 53 S 0.2374 0.3278 0.4348 54 I 0.2438 0.3054 0.4508 55 V 0.2711 0.1718 0.5571 56 H 0.3044 0.1072 0.5884 57 I 0.2705 0.0684 0.6611 58 P 0.1838 0.1879 0.6282 59 A 0.1454 0.1897 0.6649 60 S 0.2965 0.1726 0.5309 61 I 0.4339 0.1125 0.4536 62 N 0.4545 0.0644 0.4812 63 V 0.3606 0.0314 0.6080 64 P 0.2163 0.0519 0.7318 65 Y 0.1014 0.4027 0.4959 66 R 0.0916 0.4079 0.5005 67 S 0.1398 0.2355 0.6247 68 H 0.1838 0.1039 0.7123 69 P 0.0747 0.3858 0.5395 70 D 0.0641 0.4208 0.5151 71 A 0.0644 0.4496 0.4860 72 F 0.0899 0.3651 0.5450 73 A 0.1472 0.2271 0.6257 74 L 0.1792 0.1336 0.6871 75 D 0.1715 0.0333 0.7952 76 P 0.0174 0.6607 0.3219 77 L 0.0111 0.8424 0.1465 78 E 0.0112 0.8920 0.0968 79 F 0.0111 0.9029 0.0859 80 E 0.0096 0.9028 0.0876 81 K 0.0100 0.8875 0.1025 82 Q 0.0193 0.7719 0.2088 83 I 0.0519 0.4868 0.4613 84 G 0.0605 0.1919 0.7475 85 I 0.1828 0.0704 0.7468 86 P 0.1929 0.1077 0.6993 87 K 0.2573 0.0558 0.6869 88 P 0.1774 0.1470 0.6756 89 D 0.1728 0.0959 0.7313 90 S 0.0782 0.3734 0.5484 91 A 0.1094 0.1842 0.7064 92 K 0.3028 0.0312 0.6660 93 E 0.5090 0.0162 0.4748 94 L 0.7851 0.0057 0.2092 95 I 0.8162 0.0047 0.1792 96 F 0.8168 0.0044 0.1788 97 Y 0.7904 0.0061 0.2034 98 C 0.6025 0.0169 0.3807 99 A 0.2914 0.1531 0.5555 100 S 0.1631 0.1538 0.6831 101 G 0.0962 0.1883 0.7155 102 K 0.1202 0.3791 0.5007 103 R 0.0952 0.5131 0.3917 104 G 0.0267 0.7927 0.1806 105 G 0.0098 0.8833 0.1069 106 E 0.0085 0.9133 0.0782 107 A 0.0083 0.9222 0.0695 108 Q 0.0083 0.9234 0.0683 109 K 0.0083 0.9240 0.0677 110 V 0.0083 0.9224 0.0693 111 A 0.0084 0.9159 0.0756 112 S 0.0090 0.8949 0.0961 113 S 0.0165 0.7885 0.1950 114 H 0.0551 0.3438 0.6012 115 G 0.0514 0.0755 0.8731 116 Y 0.1765 0.0643 0.7592 117 S 0.2155 0.1163 0.6681 118 N 0.3684 0.0867 0.5448 119 T 0.6107 0.0412 0.3480 120 S 0.6676 0.0331 0.2993 121 L 0.6592 0.0302 0.3106 122 Y 0.4169 0.0387 0.5443 123 P 0.1879 0.1908 0.6213 124 G 0.0964 0.2059 0.6977 125 S 0.1208 0.3266 0.5525 126 M 0.0489 0.7000 0.2511 127 N 0.0273 0.8343 0.1384 128 D 0.0225 0.8818 0.0958 129 W 0.0131 0.8986 0.0882 130 V 0.0117 0.8730 0.1153 131 S 0.0237 0.7678 0.2085 132 H 0.0565 0.2371 0.7064 133 G 0.0464 0.0697 0.8839 134 G 0.1621 0.0340 0.8039 135 D 0.2195 0.0639 0.7167 136 K 0.3705 0.0922 0.5373 137 L 0.4357 0.0522 0.5121 138 D 0.2933 0.0408 0.6659 139 L 0.2027 0.1773 0.6200