# This file is the result of combining several RDB files, specifically # T0429.t2k.str2.rdb (weight 1.54425) # T0429.t2k.str4.rdb (weight 0.924988) # T0429.t2k.pb.rdb (weight 0.789901) # T0429.t2k.bys.rdb (weight 0.748322) # T0429.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 T0429.t2k.str2.rdb # ============================================ # TARGET T0429 # 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 T0429.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 9.70037 # # ============================================ # Comments from T0429.t2k.str4.rdb # ============================================ # TARGET T0429 # 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 T0429.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 9.70037 # # ============================================ # Comments from T0429.t2k.pb.rdb # ============================================ # TARGET T0429 # 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 T0429.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 9.70037 # # ============================================ # Comments from T0429.t2k.bys.rdb # ============================================ # TARGET T0429 # 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 T0429.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 9.70037 # # ============================================ # Comments from T0429.t2k.alpha.rdb # ============================================ # TARGET T0429 # 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 T0429.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 9.70037 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.3362 0.0736 0.5902 2 H 0.4688 0.0728 0.4584 3 H 0.5982 0.0661 0.3357 4 H 0.6300 0.0553 0.3146 5 H 0.5478 0.0550 0.3972 6 H 0.3347 0.0633 0.6020 7 H 0.2102 0.1986 0.5913 8 S 0.1139 0.3401 0.5461 9 S 0.1087 0.2243 0.6670 10 G 0.1481 0.1476 0.7043 11 R 0.2249 0.0739 0.7012 12 E 0.1690 0.3571 0.4739 13 N 0.1716 0.3218 0.5066 14 L 0.2520 0.3640 0.3840 15 Y 0.3289 0.3024 0.3687 16 F 0.4337 0.2250 0.3413 17 Q 0.4023 0.1713 0.4264 18 G 0.3664 0.1201 0.5135 19 M 0.3159 0.1104 0.5737 20 W 0.2512 0.2437 0.5051 21 D 0.1824 0.3060 0.5117 22 E 0.2622 0.2554 0.4824 23 T 0.3251 0.1468 0.5281 24 E 0.3360 0.1138 0.5502 25 L 0.3087 0.1288 0.5625 26 G 0.2871 0.0896 0.6233 27 L 0.4574 0.0533 0.4893 28 Y 0.6848 0.0270 0.2883 29 K 0.7685 0.0186 0.2129 30 V 0.7536 0.0226 0.2237 31 N 0.6660 0.0581 0.2758 32 E 0.5235 0.1061 0.3704 33 Y 0.3582 0.1440 0.4977 34 V 0.2577 0.1627 0.5796 35 D 0.1426 0.3679 0.4895 36 A 0.1370 0.3003 0.5627 37 R 0.2143 0.1633 0.6225 38 D 0.1740 0.2827 0.5434 39 T 0.0743 0.4505 0.4752 40 N 0.1128 0.4003 0.4870 41 M 0.1739 0.1729 0.6532 42 G 0.2314 0.0853 0.6832 43 A 0.5397 0.0463 0.4140 44 W 0.7104 0.0297 0.2599 45 F 0.7245 0.0386 0.2368 46 E 0.7124 0.0385 0.2491 47 A 0.7642 0.0350 0.2007 48 Q 0.7442 0.0429 0.2129 49 V 0.7156 0.0615 0.2229 50 V 0.6292 0.1154 0.2554 51 R 0.6068 0.1156 0.2776 52 V 0.4870 0.1790 0.3340 53 T 0.4072 0.1905 0.4023 54 R 0.2968 0.2902 0.4130 55 R 0.2478 0.3273 0.4249 56 T 0.2618 0.2770 0.4612 57 A 0.1960 0.3873 0.4167 58 R 0.1583 0.4644 0.3773 59 E 0.1243 0.5573 0.3184 60 L 0.1495 0.4949 0.3556 61 Y 0.2317 0.3463 0.4220 62 A 0.2519 0.2524 0.4957 63 N 0.2654 0.1675 0.5670 64 V 0.3107 0.1235 0.5658 65 V 0.2961 0.0936 0.6103 66 L 0.2351 0.1064 0.6584 67 G 0.1499 0.1508 0.6993 68 D 0.1431 0.2051 0.6517 69 D 0.1503 0.2266 0.6230 70 S 0.1842 0.2555 0.5604 71 L 0.1858 0.2606 0.5536 72 N 0.1579 0.2327 0.6094 73 D 0.1493 0.1473 0.7034 74 C 0.3731 0.0609 0.5661 75 R 0.5878 0.0329 0.3793 76 I 0.7014 0.0241 0.2745 77 I 0.7093 0.0294 0.2614 78 F 0.6316 0.0507 0.3177 79 V 0.4005 0.2451 0.3544 80 D 0.3013 0.3663 0.3323 81 E 0.2847 0.4232 0.2921 82 V 0.3583 0.3730 0.2687 83 F 0.4525 0.2735 0.2740 84 K 0.4869 0.2246 0.2885 85 I 0.4798 0.1785 0.3417 86 E 0.3835 0.1268 0.4897 87 R 0.2686 0.0596 0.6718 88 P 0.1503 0.1316 0.7181 89 G 0.0790 0.1206 0.8004 90 E 0.1907 0.1094 0.6999