# This file is the result of combining several RDB files, specifically # T0302.t06.dssp-ebghstl.rdb (weight 1.53986) # T0302.t06.stride-ebghtl.rdb (weight 1.24869) # T0302.t06.str2.rdb (weight 1.54758) # T0302.t06.alpha.rdb (weight 0.659012) # T0302.t04.dssp-ebghstl.rdb (weight 1.53986) # T0302.t04.stride-ebghtl.rdb (weight 1.24869) # T0302.t04.str2.rdb (weight 1.54758) # T0302.t04.alpha.rdb (weight 0.659012) # T0302.t2k.dssp-ebghstl.rdb (weight 1.53986) # T0302.t2k.stride-ebghtl.rdb (weight 1.24869) # T0302.t2k.str2.rdb (weight 1.54758) # T0302.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 T0302.t06.dssp-ebghstl.rdb # ============================================ # TARGET T0302 # Using neural net t06-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 T0302.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 386 # # ============================================ # Comments from T0302.t06.stride-ebghtl.rdb # ============================================ # TARGET T0302 # Using neural net t06-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 T0302.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 386 # # ============================================ # Comments from T0302.t06.str2.rdb # ============================================ # TARGET T0302 # Using neural net t06-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 T0302.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 386 # # ============================================ # Comments from T0302.t06.alpha.rdb # ============================================ # TARGET T0302 # Using neural net t06-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 T0302.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 386 # # ============================================ # Comments from T0302.t04.dssp-ebghstl.rdb # ============================================ # TARGET T0302 # Using neural net t06-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 T0302.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 386 # # ============================================ # Comments from T0302.t04.stride-ebghtl.rdb # ============================================ # TARGET T0302 # 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 T0302.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 386 # # ============================================ # Comments from T0302.t04.str2.rdb # ============================================ # TARGET T0302 # Using neural net t06-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 T0302.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 386 # # ============================================ # Comments from T0302.t04.alpha.rdb # ============================================ # TARGET T0302 # 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 T0302.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 386 # # ============================================ # Comments from T0302.t2k.dssp-ebghstl.rdb # ============================================ # TARGET T0302 # 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 T0302.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 342 # # ============================================ # Comments from T0302.t2k.stride-ebghtl.rdb # ============================================ # TARGET T0302 # 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 T0302.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 342 # # ============================================ # Comments from T0302.t2k.str2.rdb # ============================================ # TARGET T0302 # 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 T0302.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 342 # # ============================================ # Comments from T0302.t2k.alpha.rdb # ============================================ # TARGET T0302 # 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 T0302.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 342 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 S 0.0914 0.0412 0.8674 2 M 0.1200 0.0393 0.8408 3 V 0.1055 0.0477 0.8468 4 S 0.0665 0.0753 0.8582 5 P 0.0285 0.7426 0.2289 6 E 0.0256 0.8065 0.1679 7 E 0.0237 0.8297 0.1465 8 A 0.0254 0.8570 0.1176 9 V 0.0181 0.8324 0.1495 10 K 0.0264 0.7357 0.2378 11 W 0.0243 0.6644 0.3113 12 G 0.0373 0.4747 0.4881 13 E 0.0498 0.4515 0.4987 14 S 0.0782 0.3646 0.5572 15 F 0.0056 0.9397 0.0548 16 D 0.0051 0.9509 0.0439 17 K 0.0057 0.9431 0.0512 18 L 0.0062 0.9305 0.0633 19 L 0.0109 0.7366 0.2526 20 S 0.0173 0.4751 0.5076 21 H 0.0700 0.1244 0.8056 22 R 0.0094 0.8555 0.1350 23 D 0.0099 0.8491 0.1410 24 G 0.0093 0.9017 0.0890 25 L 0.0050 0.9544 0.0406 26 E 0.0047 0.9585 0.0368 27 A 0.0047 0.9590 0.0363 28 F 0.0047 0.9588 0.0365 29 T 0.0047 0.9583 0.0370 30 R 0.0048 0.9468 0.0483 31 F 0.0051 0.9266 0.0684 32 L 0.0087 0.8976 0.0937 33 K 0.0088 0.8559 0.1353 34 T 0.0174 0.7725 0.2102 35 E 0.0268 0.6126 0.3606 36 F 0.0412 0.3265 0.6323 37 S 0.0460 0.4100 0.5440 38 E 0.0089 0.8050 0.1861 39 E 0.0093 0.8409 0.1498 40 N 0.0125 0.8403 0.1472 41 I 0.0130 0.9081 0.0789 42 E 0.0099 0.9286 0.0615 43 F 0.0079 0.9422 0.0499 44 W 0.0060 0.9530 0.0410 45 I 0.0057 0.9536 0.0406 46 A 0.0061 0.9505 0.0435 47 C 0.0063 0.9462 0.0475 48 E 0.0067 0.9449 0.0483 49 D 0.0072 0.9207 0.0721 50 F 0.0117 0.8985 0.0898 51 K 0.0142 0.8579 0.1279 52 K 0.0172 0.7632 0.2196 53 S 0.0306 0.5956 0.3737 54 K 0.0437 0.3055 0.6508 55 G 0.0547 0.1158 0.8295 56 P 0.0192 0.6187 0.3621 57 Q 0.0090 0.7925 0.1985 58 Q 0.0113 0.8388 0.1499 59 I 0.0099 0.8843 0.1058 60 H 0.0052 0.9398 0.0550 61 L 0.0048 0.9470 0.0481 62 K 0.0048 0.9470 0.0483 63 A 0.0047 0.9539 0.0413 64 K 0.0047 0.9570 0.0383 65 A 0.0047 0.9548 0.0405 66 I 0.0048 0.9529 0.0423 67 Y 0.0052 0.9474 0.0474 68 E 0.0060 0.9391 0.0549 69 K 0.0077 0.9135 0.0787 70 F 0.0148 0.8593 0.1258 71 I 0.0433 0.7251 0.2316 72 Q 0.0638 0.4771 0.4591 73 T 0.0255 0.2634 0.7111 74 D 0.0294 0.0635 0.9072 75 A 0.0824 0.0308 0.8868 76 P 0.1309 0.0366 0.8325 77 K 0.1990 0.0567 0.7443 78 E 0.3851 0.0506 0.5643 79 V 0.4415 0.0389 0.5196 80 N 0.3293 0.0259 0.6448 81 L 0.1826 0.0591 0.7583 82 D 0.0846 0.0626 0.8528 83 F 0.0063 0.8783 0.1154 84 H 0.0058 0.9137 0.0806 85 T 0.0058 0.9399 0.0543 86 K 0.0050 0.9540 0.0410 87 E 0.0052 0.9535 0.0413 88 V 0.0056 0.9494 0.0450 89 I 0.0062 0.9324 0.0614 90 T 0.0076 0.9145 0.0779 91 N 0.0073 0.8458 0.1469 92 S 0.0120 0.7311 0.2569 93 I 0.0335 0.5519 0.4146 94 T 0.0367 0.3608 0.6026 95 Q 0.0451 0.1319 0.8230 96 P 0.0505 0.1015 0.8480 97 T 0.0716 0.1087 0.8197 98 L 0.0149 0.6488 0.3363 99 H 0.0122 0.7348 0.2530 100 S 0.0110 0.8276 0.1614 101 F 0.0079 0.8883 0.1038 102 D 0.0051 0.9414 0.0535 103 A 0.0048 0.9486 0.0466 104 A 0.0048 0.9552 0.0400 105 Q 0.0048 0.9590 0.0362 106 S 0.0048 0.9591 0.0361 107 R 0.0047 0.9597 0.0356 108 V 0.0047 0.9595 0.0358 109 Y 0.0047 0.9585 0.0368 110 Q 0.0047 0.9533 0.0420 111 L 0.0050 0.9418 0.0532 112 M 0.0061 0.9176 0.0763 113 E 0.0071 0.8721 0.1208 114 Q 0.0176 0.7739 0.2085 115 D 0.0314 0.5959 0.3727 116 S 0.0342 0.4732 0.4926 117 Y 0.0602 0.4013 0.5385 118 T 0.0185 0.6791 0.3024 119 R 0.0171 0.7238 0.2591 120 F 0.0254 0.7279 0.2468 121 L 0.0442 0.6213 0.3345 122 K 0.0389 0.4306 0.5305 123 S 0.0550 0.3936 0.5514 124 D 0.0070 0.8940 0.0990 125 I 0.0059 0.9252 0.0689 126 Y 0.0055 0.9359 0.0587 127 L 0.0057 0.9364 0.0579 128 D 0.0086 0.9252 0.0663 129 L 0.0091 0.8978 0.0932 130 M 0.0212 0.7636 0.2152 131 E 0.0247 0.4731 0.5022 132 G 0.0330 0.0983 0.8687