# This file is the result of combining several RDB files, specifically # T0437.t04.str2.rdb (weight 1.54425) # T0437.t04.str4.rdb (weight 0.924988) # T0437.t04.pb.rdb (weight 0.789901) # T0437.t04.bys.rdb (weight 0.748322) # T0437.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 T0437.t04.str2.rdb # ============================================ # TARGET T0437 # 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 T0437.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 16.5273 # # ============================================ # Comments from T0437.t04.str4.rdb # ============================================ # TARGET T0437 # 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 T0437.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 16.5273 # # ============================================ # Comments from T0437.t04.pb.rdb # ============================================ # TARGET T0437 # 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 T0437.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 16.5273 # # ============================================ # Comments from T0437.t04.bys.rdb # ============================================ # TARGET T0437 # 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 T0437.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 16.5273 # # ============================================ # Comments from T0437.t04.alpha.rdb # ============================================ # TARGET T0437 # 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 T0437.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 16.5273 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.1993 0.1356 0.6651 2 K 0.1792 0.1871 0.6337 3 D 0.2212 0.1749 0.6039 4 V 0.2571 0.2797 0.4632 5 V 0.2748 0.3157 0.4095 6 D 0.2504 0.3465 0.4031 7 K 0.2872 0.2891 0.4237 8 C 0.2459 0.2739 0.4802 9 S 0.1721 0.3280 0.4999 10 T 0.1532 0.2905 0.5563 11 K 0.1878 0.1634 0.6488 12 G 0.2197 0.1000 0.6804 13 C 0.4195 0.0779 0.5027 14 A 0.5862 0.0620 0.3517 15 I 0.6740 0.0326 0.2934 16 D 0.5971 0.0356 0.3673 17 I 0.5234 0.0946 0.3820 18 G 0.4479 0.1060 0.4461 19 T 0.6702 0.0584 0.2714 20 V 0.6796 0.0480 0.2724 21 I 0.6104 0.0487 0.3409 22 D 0.3075 0.0689 0.6237 23 N 0.1548 0.2084 0.6368 24 D 0.1116 0.2139 0.6745 25 N 0.1899 0.1359 0.6742 26 C 0.3261 0.1088 0.5651 27 T 0.5204 0.1125 0.3671 28 S 0.6804 0.0602 0.2594 29 K 0.7249 0.0531 0.2220 30 F 0.7136 0.0418 0.2446 31 S 0.6622 0.0930 0.2448 32 R 0.6832 0.0855 0.2313 33 F 0.5815 0.1197 0.2987 34 F 0.4019 0.1480 0.4501 35 A 0.1965 0.2050 0.5986 36 T 0.1515 0.1778 0.6707 37 R 0.0193 0.7283 0.2524 38 E 0.0098 0.8634 0.1267 39 E 0.0095 0.9140 0.0764 40 A 0.0085 0.9182 0.0733 41 E 0.0083 0.9217 0.0700 42 S 0.0083 0.9211 0.0706 43 F 0.0084 0.9197 0.0719 44 M 0.0084 0.9198 0.0719 45 T 0.0083 0.9143 0.0774 46 K 0.0085 0.8991 0.0924 47 L 0.0085 0.9136 0.0779 48 K 0.0084 0.9147 0.0769 49 E 0.0084 0.9165 0.0752 50 L 0.0087 0.9128 0.0786 51 A 0.0101 0.8992 0.0907 52 A 0.0124 0.8540 0.1336 53 A 0.0320 0.7515 0.2165 54 A 0.0842 0.5780 0.3378 55 S 0.1150 0.3900 0.4950 56 S 0.1537 0.2285 0.6178 57 A 0.0928 0.3566 0.5506 58 D 0.1110 0.3266 0.5624 59 E 0.1269 0.2524 0.6207 60 G 0.1485 0.1297 0.7218 61 A 0.3386 0.0723 0.5892 62 S 0.5587 0.0423 0.3990 63 V 0.6482 0.0303 0.3214 64 A 0.6325 0.0450 0.3225 65 Y 0.6730 0.0393 0.2877 66 K 0.6671 0.0402 0.2927 67 I 0.6139 0.0547 0.3314 68 K 0.5039 0.0753 0.4208 69 D 0.4469 0.0837 0.4693 70 L 0.2846 0.2201 0.4954 71 E 0.1892 0.1993 0.6114 72 G 0.1374 0.1222 0.7404 73 Q 0.4361 0.0502 0.5137 74 V 0.6963 0.0143 0.2894 75 E 0.7588 0.0084 0.2328 76 L 0.8001 0.0068 0.1931 77 D 0.7940 0.0071 0.1989 78 A 0.8072 0.0051 0.1877 79 A 0.7993 0.0059 0.1948 80 F 0.7907 0.0059 0.2034 81 T 0.7539 0.0098 0.2363 82 F 0.7209 0.0227 0.2564 83 S 0.6086 0.0695 0.3220 84 C 0.4569 0.2359 0.3071 85 Q 0.3560 0.3825 0.2615 86 A 0.2146 0.5630 0.2224 87 E 0.1503 0.7198 0.1299 88 M 0.2096 0.6745 0.1159 89 I 0.2298 0.6615 0.1087 90 I 0.2230 0.6696 0.1075 91 F 0.2168 0.6703 0.1129 92 E 0.1401 0.7477 0.1122 93 L 0.1436 0.7214 0.1350 94 S 0.1187 0.6719 0.2094 95 L 0.0734 0.6853 0.2413 96 R 0.0587 0.7094 0.2319 97 S 0.0863 0.6366 0.2770 98 L 0.0835 0.5992 0.3174 99 A 0.1067 0.4652 0.4281