# This file is the result of combining several RDB files, specifically # T0465.t06.str2.rdb (weight 1.54425) # T0465.t06.str4.rdb (weight 0.924988) # T0465.t06.pb.rdb (weight 0.789901) # T0465.t06.bys.rdb (weight 0.748322) # T0465.t06.alpha.rdb (weight 0.678173) # T0465.t04.str2.rdb (weight 1.54425) # T0465.t04.str4.rdb (weight 0.924988) # T0465.t04.pb.rdb (weight 0.789901) # T0465.t04.bys.rdb (weight 0.748322) # T0465.t04.alpha.rdb (weight 0.678173) # T0465.t2k.str2.rdb (weight 1.54425) # T0465.t2k.str4.rdb (weight 0.924988) # T0465.t2k.pb.rdb (weight 0.789901) # T0465.t2k.bys.rdb (weight 0.748322) # T0465.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 T0465.t06.str2.rdb # ============================================ # TARGET T0465 # 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 T0465.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 35.5806 # # ============================================ # Comments from T0465.t06.str4.rdb # ============================================ # TARGET T0465 # 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 T0465.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 35.5806 # # ============================================ # Comments from T0465.t06.pb.rdb # ============================================ # TARGET T0465 # 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 T0465.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 35.5806 # # ============================================ # Comments from T0465.t06.bys.rdb # ============================================ # TARGET T0465 # 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 T0465.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 35.5806 # # ============================================ # Comments from T0465.t06.alpha.rdb # ============================================ # TARGET T0465 # 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 T0465.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 35.5806 # # ============================================ # Comments from T0465.t04.str2.rdb # ============================================ # TARGET T0465 # 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 T0465.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 35.4237 # # ============================================ # Comments from T0465.t04.str4.rdb # ============================================ # TARGET T0465 # 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 T0465.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 35.4237 # # ============================================ # Comments from T0465.t04.pb.rdb # ============================================ # TARGET T0465 # 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 T0465.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 35.4237 # # ============================================ # Comments from T0465.t04.bys.rdb # ============================================ # TARGET T0465 # 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 T0465.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 35.4237 # # ============================================ # Comments from T0465.t04.alpha.rdb # ============================================ # TARGET T0465 # 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 T0465.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 35.4237 # # ============================================ # Comments from T0465.t2k.str2.rdb # ============================================ # TARGET T0465 # 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 T0465.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 25.3763 # # ============================================ # Comments from T0465.t2k.str4.rdb # ============================================ # TARGET T0465 # 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 T0465.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 25.3763 # # ============================================ # Comments from T0465.t2k.pb.rdb # ============================================ # TARGET T0465 # 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 T0465.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 25.3763 # # ============================================ # Comments from T0465.t2k.bys.rdb # ============================================ # TARGET T0465 # 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 T0465.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 25.3763 # # ============================================ # Comments from T0465.t2k.alpha.rdb # ============================================ # TARGET T0465 # 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 T0465.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 25.3763 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.2596 0.1174 0.6229 2 S 0.1836 0.1262 0.6902 3 E 0.0567 0.5859 0.3574 4 N 0.0581 0.6191 0.3228 5 Q 0.0769 0.6227 0.3004 6 N 0.0987 0.5379 0.3634 7 E 0.1549 0.4566 0.3885 8 K 0.1936 0.3640 0.4424 9 V 0.2351 0.3437 0.4212 10 Y 0.2982 0.2893 0.4125 11 D 0.2914 0.2830 0.4256 12 L 0.1583 0.5724 0.2693 13 S 0.1324 0.6149 0.2527 14 F 0.1688 0.5179 0.3133 15 F 0.2119 0.3228 0.4654 16 M 0.1872 0.0958 0.7170 17 P 0.1026 0.2953 0.6021 18 G 0.0433 0.2505 0.7063 19 Q 0.1141 0.3168 0.5691 20 T 0.1878 0.3289 0.4833 21 I 0.2202 0.3556 0.4242 22 D 0.1783 0.3345 0.4872 23 A 0.0949 0.5362 0.3690 24 E 0.1104 0.4575 0.4321 25 E 0.1937 0.2598 0.5464 26 V 0.3283 0.1161 0.5556 27 E 0.3541 0.0883 0.5576 28 V 0.3607 0.0295 0.6098 29 P 0.2912 0.0643 0.6445 30 I 0.3527 0.0996 0.5477 31 S 0.2577 0.1277 0.6146 32 K 0.2219 0.4209 0.3572 33 R 0.2939 0.3804 0.3257 34 F 0.4751 0.1929 0.3320 35 V 0.5498 0.1153 0.3349 36 D 0.3763 0.1038 0.5199 37 K 0.1366 0.3717 0.4917 38 E 0.0770 0.1869 0.7361 39 G 0.0734 0.0905 0.8361 40 N 0.2818 0.0324 0.6859 41 V 0.5762 0.0350 0.3888 42 V 0.5489 0.0183 0.4328 43 P 0.5345 0.0201 0.4453 44 F 0.6015 0.0206 0.3779 45 I 0.7309 0.0147 0.2544 46 F 0.7288 0.0144 0.2568 47 K 0.6510 0.0279 0.3210 48 A 0.4998 0.0613 0.4389 49 I 0.3144 0.0715 0.6142 50 T 0.1829 0.0312 0.7860 51 T 0.0293 0.6191 0.3516 52 D 0.0180 0.7997 0.1823 53 R 0.0191 0.8587 0.1222 54 I 0.0105 0.9020 0.0876 55 D 0.0087 0.9171 0.0742 56 E 0.0096 0.9145 0.0759 57 L 0.0109 0.9071 0.0820 58 E 0.0108 0.8943 0.0949 59 K 0.0151 0.8269 0.1580 60 E 0.0329 0.5362 0.4309 61 N 0.0929 0.2770 0.6301 62 T 0.2087 0.1535 0.6378 63 T 0.3376 0.1218 0.5407 64 Y 0.5034 0.0922 0.4044 65 K 0.5826 0.0889 0.3285 66 N 0.5365 0.0856 0.3779 67 V 0.4362 0.0983 0.4655 68 K 0.2340 0.1141 0.6519 69 G 0.1333 0.1057 0.7610 70 R 0.1765 0.1167 0.7068 71 G 0.3046 0.0829 0.6125 72 R 0.5043 0.0676 0.4281 73 V 0.5180 0.1158 0.3662 74 K 0.4404 0.2034 0.3562 75 E 0.4177 0.2066 0.3756 76 L 0.3474 0.1685 0.4842 77 D 0.1842 0.1122 0.7037 78 S 0.0299 0.6136 0.3565 79 Q 0.0194 0.7602 0.2204 80 R 0.0225 0.8304 0.1471 81 F 0.0189 0.8754 0.1057 82 Y 0.0208 0.8807 0.0985 83 A 0.0146 0.8983 0.0872 84 R 0.0206 0.8916 0.0878 85 I 0.0619 0.8314 0.1067 86 A 0.1355 0.7477 0.1169 87 V 0.2494 0.6136 0.1370 88 E 0.2539 0.5311 0.2150 89 T 0.3561 0.3191 0.3248 90 T 0.4054 0.1806 0.4140 91 V 0.4238 0.1129 0.4632 92 Y 0.3441 0.0762 0.5797 93 P 0.1721 0.1831 0.6448 94 T 0.1428 0.1720 0.6852 95 F 0.0951 0.3526 0.5523 96 K 0.0755 0.3192 0.6052 97 A 0.1280 0.2706 0.6014 98 K 0.0124 0.7502 0.2375 99 E 0.0106 0.8307 0.1587 100 L 0.0122 0.8872 0.1006 101 R 0.0100 0.8944 0.0956 102 E 0.0112 0.8711 0.1177 103 A 0.0261 0.7323 0.2416 104 Y 0.0678 0.4108 0.5214 105 K 0.0638 0.1562 0.7799 106 T 0.1579 0.1205 0.7215 107 E 0.1576 0.1471 0.6953 108 D 0.1594 0.0406 0.8001 109 P 0.0135 0.7378 0.2487 110 V 0.0101 0.8622 0.1277 111 E 0.0086 0.9173 0.0741 112 V 0.0085 0.9195 0.0720 113 A 0.0087 0.9160 0.0753 114 K 0.0098 0.9118 0.0784 115 R 0.0115 0.8919 0.0966 116 V 0.0281 0.7824 0.1895 117 L 0.0668 0.6130 0.3201 118 S 0.0894 0.4025 0.5081 119 V 0.0902 0.3962 0.5136 120 G 0.0689 0.2599 0.6712 121 G 0.0594 0.2329 0.7078 122 E 0.1164 0.3774 0.5062 123 Y 0.1043 0.6019 0.2937 124 A 0.0389 0.7878 0.1732 125 N 0.0226 0.8467 0.1307 126 W 0.0167 0.8661 0.1172 127 L 0.0171 0.8802 0.1027 128 N 0.0170 0.8794 0.1036 129 K 0.0243 0.8617 0.1140 130 A 0.0370 0.8377 0.1252 131 I 0.0635 0.7784 0.1581 132 E 0.0988 0.6698 0.2314 133 I 0.1358 0.4459 0.4184 134 N 0.1187 0.1906 0.6907 135 G 0.0807 0.1425 0.7768 136 F 0.1639 0.1291 0.7070 137 D 0.1454 0.1835 0.6711 138 D 0.0619 0.3709 0.5672 139 D 0.0831 0.3472 0.5698 140 L 0.0184 0.7595 0.2221 141 E 0.0134 0.8515 0.1350 142 D 0.0155 0.8574 0.1271 143 L 0.0137 0.8838 0.1025 144 E 0.0085 0.9109 0.0805 145 E 0.0083 0.9225 0.0692 146 A 0.0084 0.9217 0.0699 147 A 0.0085 0.9161 0.0754 148 K 0.0089 0.9062 0.0849 149 N 0.0139 0.8379 0.1482 150 L 0.0323 0.7614 0.2062 151 E 0.0464 0.6535 0.3001 152 H 0.0823 0.4422 0.4755 153 H 0.1170 0.2735 0.6095 154 H 0.1172 0.2279 0.6549 155 H 0.1218 0.2110 0.6672 156 H 0.1401 0.1707 0.6892 157 H 0.1594 0.1166 0.7240