# This file is the result of combining several RDB files, specifically # TR429.t04.str2.rdb (weight 1.54425) # TR429.t04.str4.rdb (weight 0.924988) # TR429.t04.pb.rdb (weight 0.789901) # TR429.t04.bys.rdb (weight 0.748322) # TR429.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 TR429.t04.str2.rdb # ============================================ # TARGET TR429 # 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 TR429.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 4.20324 # # ============================================ # Comments from TR429.t04.str4.rdb # ============================================ # TARGET TR429 # 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 TR429.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 4.20324 # # ============================================ # Comments from TR429.t04.pb.rdb # ============================================ # TARGET TR429 # 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 TR429.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 4.20324 # # ============================================ # Comments from TR429.t04.bys.rdb # ============================================ # TARGET TR429 # 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 TR429.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 4.20324 # # ============================================ # Comments from TR429.t04.alpha.rdb # ============================================ # TARGET TR429 # 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 TR429.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 4.20324 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 E 0.2206 0.0842 0.6952 2 T 0.1567 0.2731 0.5703 3 E 0.1648 0.2215 0.6137 4 L 0.2957 0.1406 0.5637 5 G 0.4070 0.0904 0.5026 6 L 0.5763 0.0843 0.3394 7 Y 0.6428 0.0461 0.3111 8 K 0.6081 0.0406 0.3512 9 V 0.4539 0.1686 0.3776 10 N 0.2823 0.2998 0.4179 11 E 0.2563 0.3469 0.3968 12 Y 0.3263 0.2579 0.4159 13 V 0.4444 0.1390 0.4165 14 D 0.3130 0.0958 0.5913 15 A 0.1474 0.4158 0.4368 16 R 0.1373 0.4134 0.4493 17 D 0.1837 0.3318 0.4846 18 T 0.1221 0.3529 0.5251 19 N 0.1273 0.2864 0.5863 20 M 0.1382 0.2507 0.6112 21 G 0.1748 0.2245 0.6007 22 A 0.3911 0.2456 0.3634 23 W 0.6056 0.1916 0.2028 24 F 0.6383 0.1725 0.1892 25 E 0.6390 0.1944 0.1666 26 A 0.6687 0.1608 0.1705 27 Q 0.6604 0.1609 0.1786 28 V 0.6498 0.1367 0.2135 29 V 0.5997 0.1708 0.2295 30 R 0.6134 0.1135 0.2731 31 V 0.5221 0.1216 0.3563 32 T 0.4023 0.1043 0.4934 33 R 0.2761 0.1949 0.5290 34 K 0.2184 0.1431 0.6386 35 A 0.2229 0.0717 0.7053 36 P 0.1422 0.2083 0.6495 37 S 0.1383 0.2157 0.6459 38 R 0.1352 0.2144 0.6504 39 D 0.1616 0.1409 0.6975 40 E 0.2685 0.0493 0.6822 41 P 0.2679 0.0769 0.6552 42 C 0.2675 0.1267 0.6057 43 S 0.2003 0.1709 0.6288 44 S 0.1672 0.1922 0.6406 45 T 0.1575 0.1846 0.6579 46 S 0.1768 0.1327 0.6905 47 R 0.2547 0.0717 0.6736 48 P 0.2258 0.1389 0.6353 49 A 0.2347 0.1931 0.5722 50 L 0.2116 0.2126 0.5759 51 E 0.1640 0.3157 0.5203 52 E 0.1581 0.3687 0.4732 53 D 0.2878 0.2230 0.4892 54 V 0.5411 0.0937 0.3652 55 I 0.6439 0.0634 0.2928 56 Y 0.7389 0.0313 0.2299 57 H 0.7547 0.0170 0.2283 58 V 0.7670 0.0144 0.2186 59 K 0.6447 0.0225 0.3328 60 Y 0.4866 0.0876 0.4258 61 D 0.2264 0.2205 0.5531 62 D 0.1743 0.1769 0.6488 63 Y 0.2722 0.0573 0.6705 64 P 0.1655 0.2014 0.6331 65 E 0.0907 0.3566 0.5527 66 N 0.1083 0.1597 0.7320 67 G 0.2126 0.0762 0.7112 68 V 0.5675 0.0281 0.4044 69 V 0.6961 0.0241 0.2799 70 Q 0.7377 0.0157 0.2466 71 M 0.6774 0.0306 0.2920 72 N 0.4575 0.0404 0.5022 73 S 0.2379 0.2482 0.5139 74 R 0.1590 0.2994 0.5417 75 D 0.2322 0.1777 0.5901 76 V 0.3262 0.0985 0.5753 77 R 0.3183 0.0700 0.6117 78 A 0.2431 0.2824 0.4745 79 R 0.2003 0.2630 0.5367 80 A 0.2249 0.2215 0.5536