# This file is the result of combining several RDB files, specifically # T0316.t04.dssp-ebghstl.rdb (weight 1.53986) # T0316.t04.stride-ebghtl.rdb (weight 1.24869) # T0316.t04.str2.rdb (weight 1.54758) # T0316.t04.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 T0316.t04.dssp-ebghstl.rdb # ============================================ # TARGET T0316 # 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 T0316.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 57.2788 # # ============================================ # Comments from T0316.t04.stride-ebghtl.rdb # ============================================ # TARGET T0316 # 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 T0316.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 57.2788 # # ============================================ # Comments from T0316.t04.str2.rdb # ============================================ # TARGET T0316 # 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 T0316.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 57.2788 # # ============================================ # Comments from T0316.t04.alpha.rdb # ============================================ # TARGET T0316 # 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 T0316.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 57.2788 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 A 0.1261 0.0672 0.8067 2 S 0.1141 0.1076 0.7782 3 Q 0.2749 0.1139 0.6112 4 V 0.4374 0.0782 0.4844 5 H 0.5610 0.0782 0.3607 6 F 0.5997 0.0748 0.3255 7 T 0.4960 0.0910 0.4130 8 R 0.2901 0.0918 0.6181 9 E 0.2071 0.0721 0.7208 10 M 0.1418 0.0274 0.8309 11 P 0.0917 0.0520 0.8563 12 E 0.0529 0.2143 0.7328 13 E 0.0527 0.1727 0.7746 14 F 0.1287 0.0846 0.7867 15 T 0.2714 0.0373 0.6913 16 L 0.6188 0.0146 0.3666 17 E 0.8043 0.0092 0.1865 18 C 0.8962 0.0038 0.1001 19 T 0.9188 0.0037 0.0775 20 A 0.9182 0.0037 0.0782 21 K 0.9211 0.0035 0.0753 22 F 0.9047 0.0037 0.0916 23 R 0.8348 0.0104 0.1548 24 Y 0.7220 0.0113 0.2668 25 R 0.4025 0.0202 0.5773 26 Q 0.1642 0.0220 0.8138 27 P 0.1021 0.0520 0.8458 28 D 0.1041 0.0543 0.8417 29 S 0.2621 0.0187 0.7192 30 K 0.5287 0.0097 0.4616 31 V 0.8351 0.0052 0.1597 32 T 0.9085 0.0037 0.0878 33 V 0.9170 0.0034 0.0795 34 H 0.9009 0.0038 0.0954 35 V 0.7974 0.0116 0.1910 36 K 0.3321 0.0332 0.6348 37 G 0.0755 0.0347 0.8898 38 E 0.1328 0.0600 0.8072 39 K 0.6928 0.0153 0.2919 40 T 0.8852 0.0040 0.1108 41 E 0.9198 0.0038 0.0765 42 V 0.9253 0.0032 0.0715 43 I 0.9056 0.0038 0.0907 44 F 0.8215 0.0071 0.1715 45 A 0.3938 0.0323 0.5738 46 E 0.1867 0.0274 0.7859 47 P 0.2233 0.0729 0.7039 48 Q 0.4048 0.1105 0.4847 49 R 0.5988 0.0809 0.3203 50 A 0.6719 0.0409 0.2872 51 I 0.5833 0.0347 0.3819 52 T 0.2569 0.0216 0.7215 53 P 0.0747 0.0605 0.8648 54 G 0.0934 0.0267 0.8799 55 Q 0.5707 0.0132 0.4161 56 A 0.8635 0.0049 0.1317 57 V 0.9192 0.0033 0.0776 58 V 0.9299 0.0032 0.0669 59 F 0.9057 0.0049 0.0894 60 Y 0.7852 0.0106 0.2042 61 D 0.2814 0.0219 0.6967 62 G 0.0667 0.0264 0.9070 63 E 0.2140 0.0656 0.7204 64 E 0.6703 0.0281 0.3017 65 C 0.8026 0.0240 0.1733 66 L 0.7308 0.0474 0.2218 67 G 0.5752 0.0587 0.3662 68 G 0.5389 0.0894 0.3718 69 G 0.6764 0.0941 0.2294 70 L 0.7402 0.1186 0.1411 71 I 0.6563 0.2083 0.1354 72 D 0.4854 0.2615 0.2531 73 N 0.3018 0.2704 0.4278 74 A 0.2564 0.2530 0.4906 75 Y 0.1948 0.2049 0.6003 76 R 0.1396 0.2132 0.6472 77 D 0.0866 0.2238 0.6896 78 G 0.0865 0.2008 0.7127 79 Q 0.1848 0.2436 0.5715 80 V 0.2611 0.3450 0.3939 81 C 0.2486 0.3368 0.4146 82 Q 0.2041 0.3284 0.4674 83 Y 0.1827 0.2507 0.5667 84 I 0.1043 0.1001 0.7956