# This file is the result of combining several RDB files, specifically # T0487.t2k.str2.rdb (weight 1.54425) # T0487.t2k.str4.rdb (weight 0.924988) # T0487.t2k.pb.rdb (weight 0.789901) # T0487.t2k.bys.rdb (weight 0.748322) # T0487.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 T0487.t2k.str2.rdb # ============================================ # TARGET T0487 # 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 T0487.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 1 # # ============================================ # Comments from T0487.t2k.str4.rdb # ============================================ # TARGET T0487 # 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 T0487.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 1 # # ============================================ # Comments from T0487.t2k.pb.rdb # ============================================ # TARGET T0487 # 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 T0487.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 1 # # ============================================ # Comments from T0487.t2k.bys.rdb # ============================================ # TARGET T0487 # 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 T0487.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 1 # # ============================================ # Comments from T0487.t2k.alpha.rdb # ============================================ # TARGET T0487 # 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 T0487.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 1 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 I 0.5405 0.1081 0.3514 2 L 0.5180 0.1280 0.3540 3 C 0.4501 0.1858 0.3641 4 E 0.3305 0.2613 0.4082 5 M 0.2622 0.2907 0.4470 6 S 0.1999 0.3263 0.4738 7 L 0.0749 0.6974 0.2277 8 E 0.0382 0.8231 0.1386 9 A 0.0406 0.8532 0.1062 10 W 0.0322 0.8627 0.1050 11 L 0.0372 0.8177 0.1451 12 A 0.0469 0.6739 0.2792 13 Q 0.0616 0.2364 0.7021 14 G 0.0501 0.1058 0.8440 15 H 0.1753 0.0389 0.7857 16 P 0.2127 0.0966 0.6907 17 L 0.2531 0.0660 0.6809 18 P 0.1439 0.3185 0.5376 19 K 0.0938 0.5494 0.3568 20 R 0.1366 0.5413 0.3221 21 V 0.1529 0.5538 0.2933 22 R 0.1540 0.5486 0.2974 23 N 0.1334 0.5170 0.3495 24 A 0.0906 0.5704 0.3390 25 Y 0.1151 0.4843 0.4006 26 D 0.1177 0.4479 0.4344 27 R 0.0918 0.5190 0.3892 28 R 0.1164 0.4957 0.3879 29 T 0.1536 0.5117 0.3346 30 W 0.1523 0.6087 0.2391 31 E 0.1626 0.6506 0.1868 32 L 0.1927 0.6114 0.1960 33 L 0.2214 0.5583 0.2203 34 R 0.2270 0.4440 0.3290 35 L 0.1609 0.2827 0.5563 36 G 0.1253 0.1496 0.7251 37 E 0.1425 0.2428 0.6146 38 E 0.1864 0.1871 0.6264 39 D 0.2052 0.0805 0.7143 40 P 0.0949 0.4234 0.4817 41 K 0.0853 0.4851 0.4296 42 E 0.1695 0.3059 0.5247 43 L 0.3133 0.0513 0.6354 44 P 0.2740 0.0679 0.6580 45 L 0.2373 0.0393 0.7235 46 P 0.1405 0.1943 0.6652 47 G 0.0991 0.1698 0.7311 48 G 0.1587 0.1682 0.6731 49 L 0.3153 0.1685 0.5162 50 S 0.3932 0.2034 0.4034 51 L 0.3634 0.2980 0.3386 52 L 0.3440 0.3271 0.3289 53 D 0.3157 0.3298 0.3545 54 Y 0.2627 0.3836 0.3537 55 H 0.2273 0.3431 0.4295 56 A 0.1821 0.3776 0.4402 57 S 0.1570 0.3215 0.5216 58 K 0.1270 0.2329 0.6401 59 G 0.1512 0.1579 0.6909 60 R 0.3365 0.1284 0.5351 61 L 0.4184 0.1237 0.4579 62 Q 0.3568 0.1110 0.5322 63 G 0.2750 0.0967 0.6282 64 R 0.2940 0.1162 0.5898 65 E 0.2587 0.1394 0.6019 66 G 0.1652 0.1017 0.7332 67 G 0.2934 0.0670 0.6397 68 R 0.5380 0.0424 0.4196 69 V 0.6954 0.0377 0.2669 70 A 0.7143 0.0395 0.2462 71 W 0.7322 0.0326 0.2352 72 V 0.6752 0.0578 0.2669 73 A 0.5844 0.0534 0.3622 74 D 0.2867 0.0318 0.6815 75 P 0.0846 0.3318 0.5836 76 K 0.0878 0.2618 0.6504 77 D 0.1750 0.1061 0.7188 78 P 0.0784 0.3149 0.6068 79 R 0.1127 0.2011 0.6861 80 K 0.2305 0.0676 0.7019 81 P 0.2579 0.0898 0.6523 82 I 0.3180 0.0569 0.6252 83 P 0.2466 0.2012 0.5522 84 H 0.2821 0.2165 0.5014 85 L 0.3200 0.2199 0.4601 86 T 0.2757 0.1666 0.5577 87 G 0.2925 0.1207 0.5868 88 L 0.4704 0.0666 0.4629 89 L 0.5288 0.0425 0.4287 90 V 0.4260 0.0257 0.5483 91 P 0.2363 0.0587 0.7049