# This file is the result of combining several RDB files, specifically # T0311.t06.dssp-ebghstl.rdb (weight 1.53986) # T0311.t06.stride-ebghtl.rdb (weight 1.24869) # T0311.t06.str2.rdb (weight 1.54758) # T0311.t06.alpha.rdb (weight 0.659012) # T0311.t04.dssp-ebghstl.rdb (weight 1.53986) # T0311.t04.stride-ebghtl.rdb (weight 1.24869) # T0311.t04.str2.rdb (weight 1.54758) # T0311.t04.alpha.rdb (weight 0.659012) # T0311.t2k.dssp-ebghstl.rdb (weight 1.53986) # T0311.t2k.stride-ebghtl.rdb (weight 1.24869) # T0311.t2k.str2.rdb (weight 1.54758) # T0311.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 T0311.t06.dssp-ebghstl.rdb # ============================================ # TARGET T0311 # 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 T0311.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 56.9073 # # ============================================ # Comments from T0311.t06.stride-ebghtl.rdb # ============================================ # TARGET T0311 # 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 T0311.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 56.9073 # # ============================================ # Comments from T0311.t06.str2.rdb # ============================================ # TARGET T0311 # 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 T0311.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 56.9073 # # ============================================ # Comments from T0311.t06.alpha.rdb # ============================================ # TARGET T0311 # 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 T0311.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 56.9073 # # ============================================ # Comments from T0311.t04.dssp-ebghstl.rdb # ============================================ # TARGET T0311 # 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 T0311.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 61.1882 # # ============================================ # Comments from T0311.t04.stride-ebghtl.rdb # ============================================ # TARGET T0311 # 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 T0311.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 61.1882 # # ============================================ # Comments from T0311.t04.str2.rdb # ============================================ # TARGET T0311 # 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 T0311.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 61.1882 # # ============================================ # Comments from T0311.t04.alpha.rdb # ============================================ # TARGET T0311 # 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 T0311.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 61.1882 # # ============================================ # Comments from T0311.t2k.dssp-ebghstl.rdb # ============================================ # TARGET T0311 # 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 T0311.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 219 # # ============================================ # Comments from T0311.t2k.stride-ebghtl.rdb # ============================================ # TARGET T0311 # 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 T0311.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 219 # # ============================================ # Comments from T0311.t2k.str2.rdb # ============================================ # TARGET T0311 # 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 T0311.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 48.7579 # # ============================================ # Comments from T0311.t2k.alpha.rdb # ============================================ # TARGET T0311 # 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 T0311.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 219 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.0978 0.0800 0.8221 2 K 0.1981 0.0722 0.7297 3 M 0.1826 0.0593 0.7581 4 A 0.1347 0.0578 0.8076 5 N 0.0892 0.0366 0.8742 6 H 0.0818 0.0259 0.8923 7 P 0.0989 0.0459 0.8552 8 R 0.0953 0.0587 0.8460 9 P 0.0327 0.3025 0.6648 10 G 0.0295 0.3158 0.6547 11 D 0.0933 0.5420 0.3647 12 I 0.0880 0.7197 0.1923 13 I 0.0192 0.8479 0.1329 14 Q 0.0106 0.8800 0.1094 15 E 0.0094 0.8772 0.1134 16 S 0.0139 0.8347 0.1514 17 L 0.0174 0.7912 0.1915 18 D 0.0135 0.7849 0.2016 19 E 0.0138 0.7230 0.2632 20 L 0.0519 0.3953 0.5529 21 N 0.0576 0.0536 0.8887 22 V 0.1088 0.0485 0.8426 23 S 0.1583 0.0381 0.8036 24 L 0.0052 0.9390 0.0557 25 R 0.0047 0.9558 0.0395 26 E 0.0048 0.9569 0.0384 27 F 0.0047 0.9595 0.0358 28 A 0.0048 0.9556 0.0396 29 R 0.0056 0.9378 0.0566 30 A 0.0071 0.8971 0.0959 31 M 0.0464 0.4528 0.5008 32 E 0.0379 0.0299 0.9322 33 I 0.0603 0.0165 0.9232 34 A 0.0570 0.0137 0.9293 35 P 0.0070 0.8494 0.1436 36 S 0.0061 0.8812 0.1128 37 T 0.0108 0.8957 0.0935 38 A 0.0050 0.9545 0.0405 39 S 0.0058 0.9546 0.0396 40 R 0.0052 0.9552 0.0396 41 L 0.0052 0.9510 0.0437 42 L 0.0076 0.9086 0.0838 43 T 0.0348 0.5335 0.4316 44 G 0.0258 0.2505 0.7237 45 K 0.0540 0.1534 0.7926 46 A 0.0936 0.0963 0.8101 47 A 0.1389 0.0680 0.7930 48 L 0.1237 0.0334 0.8429 49 T 0.0537 0.0333 0.9129 50 P 0.0049 0.9457 0.0494 51 E 0.0047 0.9548 0.0405 52 M 0.0047 0.9586 0.0366 53 A 0.0053 0.9590 0.0357 54 I 0.0047 0.9548 0.0405 55 K 0.0047 0.9546 0.0406 56 L 0.0047 0.9557 0.0396 57 S 0.0051 0.9473 0.0476 58 V 0.0063 0.9196 0.0741 59 V 0.0157 0.8192 0.1651 60 I 0.0433 0.4740 0.4826 61 G 0.0389 0.0856 0.8755 62 S 0.0602 0.0500 0.8898 63 S 0.0506 0.0525 0.8969 64 P 0.0056 0.9042 0.0902 65 Q 0.0049 0.9297 0.0654 66 M 0.0048 0.9476 0.0476 67 W 0.0054 0.9520 0.0426 68 L 0.0048 0.9433 0.0520 69 N 0.0048 0.9313 0.0639 70 L 0.0048 0.9300 0.0652 71 Q 0.0049 0.9228 0.0723 72 N 0.0054 0.9189 0.0757 73 A 0.0060 0.9193 0.0747 74 W 0.0067 0.9201 0.0732 75 S 0.0077 0.9169 0.0754 76 L 0.0048 0.9469 0.0484 77 A 0.0050 0.9503 0.0447 78 E 0.0050 0.9451 0.0500 79 A 0.0055 0.9398 0.0547 80 E 0.0063 0.9300 0.0637 81 K 0.0089 0.8955 0.0956 82 T 0.0161 0.8246 0.1594 83 V 0.0238 0.6689 0.3073 84 D 0.0300 0.4840 0.4860 85 V 0.0177 0.7552 0.2271 86 S 0.0181 0.7710 0.2109 87 R 0.0344 0.7818 0.1839 88 L 0.0361 0.7856 0.1782 89 R 0.0527 0.7247 0.2227 90 R 0.0720 0.6397 0.2882 91 L 0.1431 0.3461 0.5108 92 V 0.1727 0.1817 0.6456 93 T 0.1956 0.2268 0.5776 94 Q 0.1452 0.1907 0.6640 95 S 0.1362 0.1068 0.7571 96 T 0.0903 0.0527 0.8569 97 P 0.0509 0.0389 0.9102