# This file is the result of combining several RDB files, specifically # T0307.t06.dssp-ebghstl.rdb (weight 1.53986) # T0307.t06.stride-ebghtl.rdb (weight 1.24869) # T0307.t06.str2.rdb (weight 1.54758) # T0307.t06.alpha.rdb (weight 0.659012) # T0307.t04.dssp-ebghstl.rdb (weight 1.53986) # T0307.t04.stride-ebghtl.rdb (weight 1.24869) # T0307.t04.str2.rdb (weight 1.54758) # T0307.t04.alpha.rdb (weight 0.659012) # T0307.t2k.dssp-ebghstl.rdb (weight 1.53986) # T0307.t2k.stride-ebghtl.rdb (weight 1.24869) # T0307.t2k.str2.rdb (weight 1.54758) # T0307.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 T0307.t06.dssp-ebghstl.rdb # ============================================ # TARGET T0307 # 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 T0307.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 1 # # ============================================ # Comments from T0307.t06.stride-ebghtl.rdb # ============================================ # TARGET T0307 # 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 T0307.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 1 # # ============================================ # Comments from T0307.t06.str2.rdb # ============================================ # TARGET T0307 # 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 T0307.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 1 # # ============================================ # Comments from T0307.t06.alpha.rdb # ============================================ # TARGET T0307 # 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 T0307.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 1 # # ============================================ # Comments from T0307.t04.dssp-ebghstl.rdb # ============================================ # TARGET T0307 # 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 T0307.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 1 # # ============================================ # Comments from T0307.t04.stride-ebghtl.rdb # ============================================ # TARGET T0307 # 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 T0307.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 1 # # ============================================ # Comments from T0307.t04.str2.rdb # ============================================ # TARGET T0307 # 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 T0307.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 1 # # ============================================ # Comments from T0307.t04.alpha.rdb # ============================================ # TARGET T0307 # 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 T0307.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 1 # # ============================================ # Comments from T0307.t2k.dssp-ebghstl.rdb # ============================================ # TARGET T0307 # 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 T0307.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 T0307.t2k.stride-ebghtl.rdb # ============================================ # TARGET T0307 # 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 T0307.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 T0307.t2k.str2.rdb # ============================================ # TARGET T0307 # 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 T0307.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 9.66891 # # ============================================ # Comments from T0307.t2k.alpha.rdb # ============================================ # TARGET T0307 # 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 T0307.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 0.0662 0.0793 0.8545 2 G 0.1169 0.0753 0.8078 3 L 0.1200 0.0965 0.7834 4 G 0.1408 0.1012 0.7579 5 R 0.2079 0.1673 0.6248 6 Q 0.3453 0.1488 0.5059 7 S 0.4474 0.1474 0.4052 8 L 0.4125 0.2048 0.3827 9 N 0.4367 0.1904 0.3729 10 I 0.5577 0.1762 0.2661 11 M 0.5745 0.1429 0.2827 12 T 0.5352 0.1071 0.3577 13 F 0.3957 0.1017 0.5027 14 S 0.1627 0.1103 0.7270 15 G 0.0253 0.8416 0.1330 16 Q 0.0099 0.9148 0.0753 17 E 0.0059 0.9482 0.0459 18 L 0.0048 0.9575 0.0377 19 T 0.0047 0.9575 0.0378 20 A 0.0047 0.9584 0.0370 21 I 0.0047 0.9590 0.0363 22 I 0.0047 0.9579 0.0373 23 K 0.0048 0.9554 0.0397 24 M 0.0051 0.9482 0.0467 25 A 0.0075 0.9323 0.0602 26 K 0.0111 0.8970 0.0918 27 S 0.0168 0.8202 0.1630 28 M 0.0770 0.6978 0.2252 29 V 0.2107 0.5075 0.2818 30 M 0.3343 0.3044 0.3613 31 A 0.2636 0.1851 0.5513 32 D 0.1041 0.0691 0.8268 33 G 0.0629 0.0716 0.8655 34 K 0.2056 0.0290 0.7654 35 I 0.2884 0.0231 0.6886 36 K 0.0737 0.0332 0.8932 37 P 0.0052 0.9316 0.0632 38 A 0.0050 0.9454 0.0496 39 E 0.0050 0.9512 0.0438 40 I 0.0050 0.9577 0.0373 41 A 0.0048 0.9528 0.0424 42 V 0.0048 0.9472 0.0480 43 M 0.0053 0.9473 0.0475 44 T 0.0055 0.9457 0.0488 45 R 0.0056 0.9408 0.0536 46 E 0.0058 0.9322 0.0620 47 F 0.0074 0.8957 0.0969 48 M 0.0080 0.8433 0.1487 49 R 0.0146 0.7695 0.2159 50 F 0.0393 0.5214 0.4393 51 G 0.0342 0.1977 0.7680 52 I 0.0489 0.2113 0.7398 53 L 0.0558 0.2230 0.7212 54 Q 0.0135 0.7371 0.2494 55 D 0.0078 0.8369 0.1553 56 Q 0.0085 0.8885 0.1030 57 V 0.0070 0.9261 0.0669 58 D 0.0065 0.9401 0.0533 59 L 0.0076 0.9440 0.0484 60 L 0.0066 0.9458 0.0476 61 L 0.0075 0.9368 0.0557 62 K 0.0074 0.9058 0.0868 63 A 0.0091 0.8070 0.1839 64 S 0.0353 0.5432 0.4215 65 D 0.0258 0.4062 0.5680 66 S 0.0576 0.2001 0.7423 67 I 0.0651 0.1394 0.7955 68 E 0.0641 0.1464 0.7895 69 A 0.0114 0.8791 0.1095 70 S 0.0064 0.9298 0.0638 71 Q 0.0060 0.9414 0.0526 72 A 0.0055 0.9517 0.0428 73 V 0.0059 0.9539 0.0402 74 A 0.0053 0.9528 0.0420 75 L 0.0048 0.9506 0.0447 76 I 0.0049 0.9391 0.0560 77 A 0.0054 0.8604 0.1342 78 R 0.0096 0.6885 0.3019 79 M 0.0412 0.3471 0.6117 80 D 0.0376 0.3526 0.6098 81 E 0.0079 0.7948 0.1973 82 E 0.0083 0.8311 0.1606 83 R 0.0084 0.8728 0.1188 84 K 0.0055 0.9260 0.0685 85 K 0.0064 0.9373 0.0564 86 Y 0.0050 0.9384 0.0566 87 V 0.0051 0.9446 0.0503 88 A 0.0048 0.9485 0.0467 89 S 0.0049 0.9228 0.0724 90 Y 0.0053 0.9237 0.0710 91 L 0.0067 0.9206 0.0727 92 G 0.0058 0.9099 0.0844 93 V 0.0075 0.9053 0.0872 94 I 0.0159 0.8769 0.1072 95 M 0.0384 0.7498 0.2118 96 A 0.0543 0.4886 0.4572 97 S 0.0736 0.2994 0.6271 98 D 0.0552 0.1409 0.8038 99 G 0.0445 0.1046 0.8509 100 D 0.1238 0.1003 0.7759 101 I 0.1291 0.1484 0.7226 102 D 0.0631 0.1340 0.8030 103 D 0.0075 0.8208 0.1717 104 N 0.0063 0.8839 0.1097 105 E 0.0051 0.9455 0.0494 106 L 0.0047 0.9573 0.0380 107 A 0.0047 0.9570 0.0383 108 L 0.0047 0.9597 0.0356 109 W 0.0047 0.9598 0.0356 110 T 0.0047 0.9595 0.0357 111 L 0.0047 0.9595 0.0358 112 I 0.0047 0.9590 0.0363 113 S 0.0048 0.9538 0.0414 114 T 0.0057 0.9235 0.0708 115 L 0.0086 0.8487 0.1426 116 C 0.0459 0.4849 0.4692 117 G 0.0424 0.0351 0.9225 118 L 0.0641 0.0135 0.9224 119 P 0.0685 0.0184 0.9130 120 T 0.0909 0.2188 0.6903 121 M 0.1535 0.3267 0.5197 122 T 0.3048 0.3343 0.3609 123 V 0.3067 0.4739 0.2194 124 M 0.2723 0.5107 0.2170 125 E 0.2654 0.4944 0.2402 126 A 0.1430 0.5759 0.2811 127 I 0.0913 0.5722 0.3365 128 N 0.0575 0.5445 0.3980 129 N 0.0484 0.4962 0.4555 130 M 0.0563 0.4706 0.4731 131 K 0.0495 0.3617 0.5888 132 N 0.0491 0.2377 0.7132 133 L 0.0358 0.0907 0.8735