# This file is the result of combining several RDB files, specifically # T0321.t06.dssp-ebghstl.rdb (weight 1.53986) # T0321.t06.stride-ebghtl.rdb (weight 1.24869) # T0321.t06.str2.rdb (weight 1.54758) # T0321.t06.alpha.rdb (weight 0.659012) # T0321.t04.dssp-ebghstl.rdb (weight 1.53986) # T0321.t04.stride-ebghtl.rdb (weight 1.24869) # T0321.t04.str2.rdb (weight 1.54758) # T0321.t04.alpha.rdb (weight 0.659012) # T0321.t2k.dssp-ebghstl.rdb (weight 1.53986) # T0321.t2k.stride-ebghtl.rdb (weight 1.24869) # T0321.t2k.str2.rdb (weight 1.54758) # T0321.t2k.alpha.rdb (weight 0.659012) # 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 T0321.t06.dssp-ebghstl.rdb # ============================================ # TARGET T0321 # Using neural net t04-2621-IDGaaH13-3-13-7-13-9-13-11-ebghstl-dssp-seeded.net # This is a 4-layer network, with # window units # 3 13 # 7 13 # 9 13 # 11 7 (1 EBGHSTL ) # The input amino acid frequencies were determined from # alignment T0321.t06-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 31.3761 # # ============================================ # Comments from T0321.t06.stride-ebghtl.rdb # ============================================ # TARGET T0321 # Using neural net t04-2621-IDGaaH13-3-13-7-13-9-13-11-ebghtl-stride-seeded.net # This is a 4-layer network, with # window units # 3 13 # 7 13 # 9 13 # 11 6 (1 EBGHTL ) # The input amino acid frequencies were determined from # alignment T0321.t06-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 31.3761 # # ============================================ # Comments from T0321.t06.str2.rdb # ============================================ # TARGET T0321 # Using neural net dunbrack-30pc-1763-t2k-thin90-IDGaaH13-3-13-7-13-9-13-11-t1c2-str2-from-empty.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 T0321.t06-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 31.3761 # # ============================================ # Comments from T0321.t06.alpha.rdb # ============================================ # TARGET T0321 # Using neural net t04-2621-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 T0321.t06-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 31.3761 # # ============================================ # Comments from T0321.t04.dssp-ebghstl.rdb # ============================================ # TARGET T0321 # Using neural net t04-2621-IDGaaH13-3-13-7-13-9-13-11-ebghstl-dssp-seeded.net # This is a 4-layer network, with # window units # 3 13 # 7 13 # 9 13 # 11 7 (1 EBGHSTL ) # The input amino acid frequencies were determined from # alignment T0321.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 28 # # ============================================ # Comments from T0321.t04.stride-ebghtl.rdb # ============================================ # TARGET T0321 # Using neural net t04-2621-IDGaaH13-3-13-7-13-9-13-11-ebghtl-stride-seeded.net # This is a 4-layer network, with # window units # 3 13 # 7 13 # 9 13 # 11 6 (1 EBGHTL ) # The input amino acid frequencies were determined from # alignment T0321.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 28 # # ============================================ # Comments from T0321.t04.str2.rdb # ============================================ # TARGET T0321 # Using neural net dunbrack-30pc-1763-t2k-thin90-IDGaaH13-3-13-7-13-9-13-11-t1c2-str2-from-empty.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 T0321.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 28 # # ============================================ # Comments from T0321.t04.alpha.rdb # ============================================ # TARGET T0321 # Using neural net t04-2621-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 T0321.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 28 # # ============================================ # Comments from T0321.t2k.dssp-ebghstl.rdb # ============================================ # TARGET T0321 # Using neural net t2k-5740-IDaaHr-5-15-7-15-9-15-13-ebghstl-seeded.net # This is a 4-layer network, with # window units # 5 15 # 7 15 # 9 15 # 13 7 (1 EBGHSTL ) # The input amino acid frequencies were determined from # alignment T0321.t2k-thin90.a2m.gz # with weighted counts, using HenikoffWeight(-1 bits/column, 1) # Counts were regularized to probabilities using # /projects/compbio/lib/recode3.20comp # Total sequence weight for alignment was 10 # # ============================================ # Comments from T0321.t2k.stride-ebghtl.rdb # ============================================ # TARGET T0321 # Using neural net t2k-5651-IDaaHr-5-15-7-15-9-15-13-ebghtl-seeded.net # This is a 4-layer network, with # window units # 5 15 # 7 15 # 9 15 # 13 6 (1 EBGHTL ) # The input amino acid frequencies were determined from # alignment T0321.t2k-thin90.a2m.gz # with weighted counts, using HenikoffWeight(-1 bits/column, 1) # Counts were regularized to probabilities using # /projects/compbio/lib/recode3.20comp # Total sequence weight for alignment was 10 # # ============================================ # Comments from T0321.t2k.str2.rdb # ============================================ # TARGET T0321 # Using neural net dunbrack-30pc-1763-t2k-thin90-IDGaaH13-3-13-7-13-9-13-11-t1c2-str2-from-empty.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 T0321.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 10 # # ============================================ # Comments from T0321.t2k.alpha.rdb # ============================================ # TARGET T0321 # Using neural net t2k-5651-IDaaHr-5-15-7-15-9-15-13-alpha-seeded.net # This is a 4-layer network, with # window units # 5 15 # 7 15 # 9 15 # 13 11 (1 ABCDEFGHIST ) # The input amino acid frequencies were determined from # alignment T0321.t2k-thin90.a2m.gz # with weighted counts, using HenikoffWeight(-1 bits/column, 1) # Counts were regularized to probabilities using # /projects/compbio/lib/recode3.20comp # Total sequence weight for alignment was 10 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.0256 0.2488 0.7257 2 W 0.0165 0.7508 0.2327 3 E 0.0118 0.7841 0.2041 4 I 0.0129 0.8279 0.1592 5 Y 0.0147 0.8471 0.1382 6 D 0.0156 0.8938 0.0906 7 A 0.0161 0.8892 0.0946 8 M 0.0105 0.8988 0.0907 9 I 0.0148 0.8297 0.1555 10 N 0.0136 0.6243 0.3621 11 G 0.0239 0.3859 0.5902 12 I 0.0750 0.1251 0.7998 13 P 0.0543 0.1023 0.8434 14 E 0.0403 0.1839 0.7757 15 D 0.0439 0.1423 0.8138 16 F 0.1115 0.0679 0.8206 17 L 0.2438 0.0680 0.6882 18 V 0.3986 0.1325 0.4689 19 D 0.4732 0.2209 0.3059 20 E 0.6830 0.1338 0.1832 21 L 0.7823 0.0958 0.1219 22 V 0.8274 0.0524 0.1202 23 C 0.7218 0.0488 0.2294 24 G 0.4648 0.0395 0.4957 25 T 0.2860 0.0620 0.6519 26 T 0.4171 0.0476 0.5353 27 H 0.7493 0.0267 0.2240 28 S 0.8741 0.0124 0.1135 29 V 0.9121 0.0069 0.0811 30 I 0.8817 0.0130 0.1053 31 R 0.8327 0.0103 0.1569 32 S 0.4827 0.0206 0.4967 33 G 0.1006 0.0897 0.8097 34 N 0.0558 0.0580 0.8863 35 G 0.2381 0.0595 0.7023 36 V 0.4281 0.0440 0.5279 37 G 0.5827 0.0367 0.3806 38 L 0.6587 0.0301 0.3112 39 G 0.5338 0.0291 0.4371 40 P 0.4003 0.0276 0.5721 41 N 0.2009 0.0268 0.7723 42 R 0.0768 0.1294 0.7938 43 P 0.0555 0.1408 0.8037 44 F 0.0821 0.1279 0.7900 45 E 0.0906 0.0994 0.8100 46 T 0.1263 0.1026 0.7712 47 R 0.1328 0.1341 0.7332 48 M 0.1098 0.1106 0.7796 49 P 0.0731 0.1843 0.7426 50 M 0.0405 0.4388 0.5206 51 L 0.0325 0.5016 0.4659 52 T 0.0320 0.5818 0.3862 53 Q 0.0286 0.5861 0.3852 54 N 0.0351 0.5827 0.3822 55 L 0.0474 0.5064 0.4462 56 L 0.0338 0.3028 0.6634 57 G 0.0317 0.1259 0.8424 58 L 0.0982 0.0772 0.8245 59 P 0.1277 0.1342 0.7381 60 L 0.0073 0.9328 0.0600 61 R 0.0056 0.9520 0.0424 62 V 0.0055 0.9513 0.0431 63 A 0.0051 0.9502 0.0448 64 A 0.0048 0.9464 0.0488 65 G 0.0051 0.9180 0.0769 66 C 0.0056 0.8960 0.0984 67 V 0.0186 0.8221 0.1593 68 K 0.0256 0.7236 0.2508 69 S 0.0532 0.6039 0.3429 70 W 0.0518 0.4052 0.5430 71 N 0.0593 0.2696 0.6711 72 Y 0.0064 0.9013 0.0923 73 V 0.0052 0.9275 0.0672 74 E 0.0056 0.9454 0.0490 75 A 0.0069 0.9474 0.0457 76 S 0.0086 0.9396 0.0518 77 I 0.0088 0.9393 0.0519 78 G 0.0115 0.9377 0.0508 79 L 0.0234 0.9238 0.0528 80 A 0.0290 0.9166 0.0545 81 A 0.0412 0.8917 0.0671 82 I 0.0370 0.8697 0.0933 83 N 0.0658 0.8012 0.1330 84 A 0.0400 0.7946 0.1655 85 Y 0.0454 0.7227 0.2319 86 Y 0.0739 0.5801 0.3460 87 N 0.0723 0.3381 0.5896 88 N 0.0534 0.3162 0.6304 89 P 0.0225 0.7426 0.2350 90 Q 0.0187 0.7838 0.1976 91 V 0.0182 0.8102 0.1717 92 A 0.0268 0.8014 0.1718 93 R 0.0269 0.7740 0.1992 94 E 0.0226 0.7254 0.2519 95 H 0.0337 0.4502 0.5161 96 G 0.0437 0.1569 0.7994 97 V 0.0869 0.1029 0.8102 98 I 0.1690 0.1198 0.7112 99 F 0.2049 0.2195 0.5756 100 S 0.2015 0.2648 0.5337 101 D 0.1814 0.2462 0.5725 102 A 0.1906 0.2476 0.5619 103 K 0.2022 0.2158 0.5820 104 R 0.1889 0.2566 0.5545 105 V 0.1183 0.2800 0.6017 106 E 0.0902 0.3163 0.5935 107 D 0.0769 0.3674 0.5557 108 R 0.1371 0.2853 0.5776 109 M 0.2636 0.1823 0.5540 110 N 0.3058 0.1512 0.5429 111 D 0.2764 0.1691 0.5545 112 P 0.4011 0.1873 0.4116 113 F 0.6507 0.1120 0.2373 114 I 0.6910 0.0853 0.2238 115 M 0.6084 0.0731 0.3185 116 S 0.3568 0.0669 0.5764 117 Q 0.1102 0.2933 0.5965 118 N 0.0982 0.2790 0.6228 119 E 0.1913 0.3304 0.4783 120 V 0.1863 0.2721 0.5416 121 K 0.1155 0.1945 0.6900 122 G 0.0758 0.0966 0.8275 123 K 0.0667 0.0468 0.8865