# This file is the result of combining several RDB files, specifically # T0482.t06.str2.rdb (weight 1.54425) # T0482.t06.str4.rdb (weight 0.924988) # T0482.t06.pb.rdb (weight 0.789901) # T0482.t06.bys.rdb (weight 0.748322) # T0482.t06.alpha.rdb (weight 0.678173) # T0482.t04.str2.rdb (weight 1.54425) # T0482.t04.str4.rdb (weight 0.924988) # T0482.t04.pb.rdb (weight 0.789901) # T0482.t04.bys.rdb (weight 0.748322) # T0482.t04.alpha.rdb (weight 0.678173) # T0482.t2k.str2.rdb (weight 1.54425) # T0482.t2k.str4.rdb (weight 0.924988) # T0482.t2k.pb.rdb (weight 0.789901) # T0482.t2k.bys.rdb (weight 0.748322) # T0482.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 T0482.t06.str2.rdb # ============================================ # TARGET T0482 # 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 T0482.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 5.74721 # # ============================================ # Comments from T0482.t06.str4.rdb # ============================================ # TARGET T0482 # 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 T0482.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 5.74721 # # ============================================ # Comments from T0482.t06.pb.rdb # ============================================ # TARGET T0482 # 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 T0482.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 5.74721 # # ============================================ # Comments from T0482.t06.bys.rdb # ============================================ # TARGET T0482 # 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 T0482.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 5.74721 # # ============================================ # Comments from T0482.t06.alpha.rdb # ============================================ # TARGET T0482 # 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 T0482.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 5.74721 # # ============================================ # Comments from T0482.t04.str2.rdb # ============================================ # TARGET T0482 # 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 T0482.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 5.74721 # # ============================================ # Comments from T0482.t04.str4.rdb # ============================================ # TARGET T0482 # 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 T0482.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 5.74721 # # ============================================ # Comments from T0482.t04.pb.rdb # ============================================ # TARGET T0482 # 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 T0482.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 5.74721 # # ============================================ # Comments from T0482.t04.bys.rdb # ============================================ # TARGET T0482 # 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 T0482.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 5.74721 # # ============================================ # Comments from T0482.t04.alpha.rdb # ============================================ # TARGET T0482 # 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 T0482.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 5.74721 # # ============================================ # Comments from T0482.t2k.str2.rdb # ============================================ # TARGET T0482 # 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 T0482.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 6.21971 # # ============================================ # Comments from T0482.t2k.str4.rdb # ============================================ # TARGET T0482 # 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 T0482.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 6.21971 # # ============================================ # Comments from T0482.t2k.pb.rdb # ============================================ # TARGET T0482 # 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 T0482.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 6.21971 # # ============================================ # Comments from T0482.t2k.bys.rdb # ============================================ # TARGET T0482 # 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 T0482.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 6.21971 # # ============================================ # Comments from T0482.t2k.alpha.rdb # ============================================ # TARGET T0482 # 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 T0482.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 6.21971 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.3057 0.1277 0.5667 2 F 0.2997 0.0782 0.6222 3 E 0.2775 0.0578 0.6647 4 P 0.2191 0.1587 0.6222 5 G 0.2092 0.1277 0.6631 6 H 0.3815 0.1219 0.4965 7 L 0.5406 0.0893 0.3701 8 H 0.6079 0.0676 0.3245 9 L 0.5386 0.1327 0.3287 10 V 0.4960 0.1327 0.3713 11 S 0.3895 0.0954 0.5151 12 L 0.2491 0.0575 0.6934 13 P 0.1385 0.1487 0.7128 14 G 0.0925 0.1104 0.7971 15 L 0.1593 0.1428 0.6979 16 D 0.1595 0.1445 0.6960 17 Q 0.1925 0.1482 0.6593 18 Q 0.2213 0.1441 0.6346 19 D 0.3205 0.0915 0.5880 20 I 0.4696 0.0467 0.4837 21 N 0.6172 0.0232 0.3595 22 I 0.7165 0.0153 0.2682 23 H 0.7274 0.0088 0.2638 24 I 0.7628 0.0098 0.2274 25 R 0.7536 0.0119 0.2345 26 Y 0.7595 0.0145 0.2259 27 E 0.7392 0.0187 0.2421 28 V 0.6802 0.0424 0.2774 29 R 0.5733 0.0949 0.3318 30 Q 0.5042 0.0824 0.4134 31 N 0.3145 0.0608 0.6247 32 A 0.0899 0.4135 0.4967 33 E 0.0700 0.3872 0.5428 34 S 0.1234 0.1607 0.7159 35 G 0.1493 0.0818 0.7689 36 A 0.4152 0.0512 0.5336 37 Y 0.7005 0.0229 0.2765 38 V 0.7715 0.0119 0.2165 39 H 0.7874 0.0087 0.2039 40 F 0.7934 0.0075 0.1991 41 D 0.7598 0.0091 0.2311 42 M 0.7044 0.0298 0.2658 43 D 0.5769 0.0454 0.3777 44 G 0.5810 0.0401 0.3790 45 E 0.6316 0.0364 0.3320 46 I 0.5716 0.0550 0.3733 47 D 0.2870 0.0724 0.6407 48 G 0.1262 0.0802 0.7936 49 K 0.3402 0.0154 0.6444 50 P 0.4332 0.0202 0.5466 51 F 0.3554 0.1212 0.5235 52 S 0.2607 0.2309 0.5084 53 D 0.2173 0.3415 0.4412 54 S 0.2866 0.2773 0.4361 55 F 0.4235 0.0922 0.4843 56 E 0.4358 0.0581 0.5061 57 L 0.3503 0.0242 0.6255 58 P 0.1797 0.1020 0.7183 59 R 0.0422 0.6288 0.3290 60 D 0.0431 0.7019 0.2550 61 T 0.0652 0.7221 0.2128 62 A 0.0630 0.7559 0.1811 63 F 0.0560 0.7883 0.1556 64 N 0.0397 0.8049 0.1555 65 F 0.0274 0.8005 0.1721 66 A 0.0180 0.8394 0.1426 67 S 0.0119 0.8591 0.1291 68 D 0.0113 0.8734 0.1152 69 A 0.0101 0.8881 0.1018 70 T 0.0095 0.9106 0.0800 71 R 0.0086 0.9182 0.0731 72 V 0.0095 0.9151 0.0753 73 A 0.0099 0.9075 0.0826 74 Q 0.0113 0.8792 0.1095 75 K 0.0215 0.7531 0.2254 76 H 0.0575 0.2732 0.6692 77 G 0.0498 0.0887 0.8615 78 L 0.1777 0.0465 0.7757 79 H 0.2012 0.0329 0.7659 80 P 0.0946 0.3671 0.5383 81 K 0.1049 0.3628 0.5322 82 F 0.1564 0.2898 0.5538 83 G 0.1669 0.2638 0.5693 84 A 0.2033 0.3528 0.4440 85 I 0.2075 0.4135 0.3790 86 T 0.1857 0.4859 0.3285 87 R 0.1505 0.5426 0.3069 88 V 0.1222 0.5284 0.3494 89 H 0.1124 0.5102 0.3774 90 K 0.0444 0.7049 0.2507 91 E 0.0324 0.7480 0.2196 92 Y 0.0424 0.7871 0.1705 93 D 0.0191 0.8585 0.1223 94 A 0.0138 0.8575 0.1287 95 M 0.0149 0.8361 0.1489 96 F 0.0126 0.8628 0.1246 97 E 0.0097 0.8988 0.0915 98 D 0.0112 0.8947 0.0941 99 I 0.0113 0.8872 0.1015 100 R 0.0110 0.8839 0.1051 101 A 0.0136 0.8646 0.1217 102 K 0.0435 0.6919 0.2645 103 L 0.1307 0.4456 0.4237 104 H 0.2130 0.1634 0.6236 105 A 0.2343 0.0850 0.6806 106 H 0.1987 0.0485 0.7528 107 P 0.1282 0.1717 0.7001 108 G 0.0643 0.1103 0.8254 109 E 0.2163 0.0393 0.7444 110 P 0.3364 0.0373 0.6263 111 V 0.4440 0.0352 0.5208 112 D 0.1950 0.0241 0.7809 113 L 0.0423 0.6540 0.3037 114 E 0.0380 0.7161 0.2460 115 R 0.1209 0.6306 0.2485 116 I 0.1643 0.5879 0.2478 117 I 0.2433 0.4512 0.3055 118 R 0.1914 0.3544 0.4542 119 H 0.1325 0.2124 0.6551 120 E 0.1134 0.1585 0.7280