# This file is the result of combining several RDB files, specifically # T0437.t2k.str2.rdb (weight 1.54425) # T0437.t2k.str4.rdb (weight 0.924988) # T0437.t2k.pb.rdb (weight 0.789901) # T0437.t2k.bys.rdb (weight 0.748322) # T0437.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 T0437.t2k.str2.rdb # ============================================ # TARGET T0437 # 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 T0437.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 14.8244 # # ============================================ # Comments from T0437.t2k.str4.rdb # ============================================ # TARGET T0437 # 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 T0437.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 14.8244 # # ============================================ # Comments from T0437.t2k.pb.rdb # ============================================ # TARGET T0437 # 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 T0437.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 14.8244 # # ============================================ # Comments from T0437.t2k.bys.rdb # ============================================ # TARGET T0437 # 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 T0437.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 14.8244 # # ============================================ # Comments from T0437.t2k.alpha.rdb # ============================================ # TARGET T0437 # 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 T0437.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 14.8244 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.2031 0.2371 0.5599 2 K 0.1618 0.3536 0.4846 3 D 0.1851 0.3980 0.4170 4 V 0.2033 0.4031 0.3936 5 V 0.2254 0.3567 0.4179 6 D 0.1788 0.4208 0.4003 7 K 0.1711 0.4475 0.3814 8 C 0.2125 0.3601 0.4274 9 S 0.2237 0.2575 0.5188 10 T 0.2327 0.2451 0.5221 11 K 0.2376 0.1563 0.6060 12 G 0.2947 0.1008 0.6045 13 C 0.4527 0.0839 0.4634 14 A 0.5902 0.0702 0.3397 15 I 0.6574 0.0483 0.2943 16 D 0.5988 0.0428 0.3585 17 I 0.5152 0.0719 0.4128 18 G 0.5005 0.0557 0.4438 19 T 0.6504 0.0347 0.3148 20 V 0.7032 0.0243 0.2725 21 I 0.6437 0.0284 0.3279 22 D 0.3551 0.0472 0.5977 23 N 0.1637 0.1939 0.6424 24 D 0.1056 0.2211 0.6732 25 N 0.1883 0.1402 0.6715 26 C 0.3380 0.0942 0.5678 27 T 0.5704 0.0525 0.3771 28 S 0.6714 0.0339 0.2947 29 K 0.7276 0.0241 0.2483 30 F 0.7297 0.0309 0.2394 31 S 0.6728 0.0614 0.2658 32 R 0.6410 0.0999 0.2591 33 F 0.4915 0.1604 0.3481 34 F 0.3412 0.1908 0.4680 35 A 0.1669 0.3196 0.5135 36 T 0.1337 0.3091 0.5572 37 R 0.0143 0.7531 0.2326 38 E 0.0092 0.8707 0.1201 39 E 0.0084 0.9197 0.0719 40 A 0.0084 0.9201 0.0716 41 E 0.0083 0.9236 0.0681 42 S 0.0083 0.9245 0.0672 43 F 0.0083 0.9236 0.0681 44 M 0.0083 0.9210 0.0707 45 T 0.0083 0.9224 0.0693 46 K 0.0083 0.9222 0.0695 47 L 0.0084 0.9177 0.0739 48 K 0.0083 0.9218 0.0699 49 E 0.0083 0.9228 0.0689 50 L 0.0086 0.9155 0.0759 51 A 0.0091 0.9047 0.0862 52 A 0.0095 0.8850 0.1055 53 A 0.0191 0.7667 0.2142 54 A 0.0794 0.5234 0.3972 55 S 0.1142 0.3275 0.5583 56 S 0.0704 0.4194 0.5102 57 A 0.0707 0.3506 0.5787 58 D 0.1228 0.2374 0.6398 59 E 0.1485 0.2183 0.6332 60 G 0.1922 0.2066 0.6012 61 A 0.3502 0.1256 0.5241 62 S 0.5379 0.0728 0.3893 63 V 0.6409 0.0521 0.3070 64 A 0.6308 0.0598 0.3094 65 Y 0.6560 0.0747 0.2693 66 K 0.6536 0.0661 0.2803 67 I 0.6169 0.0946 0.2885 68 K 0.5656 0.1094 0.3251 69 D 0.4953 0.1306 0.3741 70 L 0.3098 0.2073 0.4830 71 E 0.2088 0.1815 0.6098 72 G 0.1252 0.1346 0.7402 73 Q 0.3813 0.0549 0.5638 74 V 0.6199 0.0170 0.3631 75 E 0.7378 0.0095 0.2527 76 L 0.7945 0.0075 0.1980 77 D 0.7812 0.0058 0.2129 78 A 0.8010 0.0066 0.1923 79 A 0.7941 0.0060 0.1999 80 F 0.7833 0.0076 0.2091 81 T 0.7739 0.0093 0.2168 82 F 0.7340 0.0153 0.2507 83 S 0.6714 0.0375 0.2911 84 C 0.5897 0.0852 0.3251 85 Q 0.4763 0.1933 0.3304 86 A 0.4065 0.3368 0.2567 87 E 0.2876 0.4974 0.2149 88 M 0.3897 0.4472 0.1631 89 I 0.2987 0.5376 0.1637 90 I 0.2925 0.5618 0.1457 91 F 0.2944 0.5448 0.1608 92 E 0.2359 0.5450 0.2191 93 L 0.2159 0.4883 0.2958 94 S 0.1417 0.4584 0.3998 95 L 0.0935 0.5819 0.3245 96 R 0.0863 0.6173 0.2964 97 S 0.0917 0.5725 0.3359 98 L 0.0905 0.5135 0.3960 99 A 0.0972 0.4681 0.4347