# This file is the result of combining several RDB files, specifically # T0320.t06.dssp-ebghstl.rdb (weight 1.53986) # T0320.t06.stride-ebghtl.rdb (weight 1.24869) # T0320.t06.str2.rdb (weight 1.54758) # T0320.t06.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 T0320.t06.dssp-ebghstl.rdb # ============================================ # TARGET T0320 # 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 T0320.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 3.37338 # # ============================================ # Comments from T0320.t06.stride-ebghtl.rdb # ============================================ # TARGET T0320 # 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 T0320.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 3.37338 # # ============================================ # Comments from T0320.t06.str2.rdb # ============================================ # TARGET T0320 # 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 T0320.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 3.37338 # # ============================================ # Comments from T0320.t06.alpha.rdb # ============================================ # TARGET T0320 # 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 T0320.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 3.37338 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 N 0.0565 0.0356 0.9078 2 E 0.2431 0.0269 0.7300 3 P 0.3668 0.0298 0.6033 4 I 0.5591 0.0692 0.3717 5 C 0.4849 0.1300 0.3851 6 G 0.4091 0.1733 0.4176 7 L 0.4345 0.1659 0.3996 8 Y 0.3983 0.1225 0.4792 9 G 0.2975 0.1024 0.6001 10 K 0.1974 0.1094 0.6933 11 G 0.2288 0.0829 0.6883 12 F 0.4693 0.0548 0.4759 13 T 0.5859 0.0587 0.3554 14 S 0.5382 0.0594 0.4024 15 I 0.3352 0.1267 0.5381 16 G 0.1987 0.1004 0.7009 17 G 0.2221 0.1149 0.6630 18 I 0.2244 0.2226 0.5531 19 N 0.1628 0.2257 0.6115 20 N 0.1172 0.1927 0.6901 21 S 0.1554 0.1177 0.7269 22 L 0.1287 0.0423 0.8289 23 P 0.1064 0.0554 0.8382 24 N 0.1305 0.0687 0.8008 25 P 0.0506 0.2775 0.6719 26 H 0.1170 0.2801 0.6029 27 L 0.2450 0.1993 0.5557 28 R 0.2769 0.1039 0.6192 29 K 0.2518 0.0988 0.6494 30 D 0.0846 0.0774 0.8380 31 S 0.0542 0.1069 0.8389 32 N 0.0670 0.0813 0.8517 33 N 0.0966 0.0460 0.8573 34 P 0.0572 0.1559 0.7869 35 A 0.1962 0.1875 0.6163 36 L 0.3595 0.0808 0.5597 37 H 0.4067 0.0323 0.5610 38 F 0.6078 0.0338 0.3583 39 E 0.6973 0.0575 0.2452 40 W 0.8320 0.0486 0.1194 41 E 0.8415 0.0630 0.0956 42 I 0.7487 0.1421 0.1092 43 I 0.6570 0.1704 0.1725 44 H 0.4680 0.1933 0.3387 45 A 0.2099 0.2401 0.5500 46 F 0.1199 0.1777 0.7024 47 G 0.1050 0.0849 0.8101 48 K 0.1235 0.1623 0.7143 49 D 0.1054 0.1907 0.7038 50 A 0.0577 0.3170 0.6253 51 E 0.0639 0.2657 0.6704 52 G 0.0667 0.2128 0.7205 53 E 0.1269 0.2289 0.6441 54 R 0.2065 0.2382 0.5553 55 S 0.1721 0.2549 0.5729 56 S 0.1245 0.3208 0.5547 57 A 0.1713 0.3236 0.5051 58 I 0.2319 0.2404 0.5277 59 N 0.1877 0.1620 0.6503 60 T 0.1219 0.1405 0.7376 61 S 0.1236 0.0610 0.8154 62 P 0.1199 0.1363 0.7438 63 I 0.2785 0.1572 0.5644 64 S 0.4482 0.1652 0.3866 65 V 0.4758 0.1968 0.3274 66 V 0.4082 0.1738 0.4180 67 D 0.2943 0.1575 0.5482 68 K 0.0869 0.6264 0.2867 69 E 0.0757 0.6327 0.2916 70 R 0.0984 0.5846 0.3170 71 F 0.0915 0.5942 0.3143 72 S 0.0695 0.5863 0.3442 73 K 0.0707 0.5590 0.3703 74 Y 0.1015 0.4437 0.4548 75 H 0.0892 0.3643 0.5465 76 D 0.0496 0.3813 0.5692 77 N 0.0587 0.2514 0.6899 78 Y 0.1441 0.1398 0.7160 79 Y 0.1530 0.0356 0.8114 80 P 0.1346 0.0740 0.7914 81 G 0.3034 0.0547 0.6418 82 W 0.6864 0.0395 0.2741 83 Y 0.8247 0.0387 0.1366 84 L 0.8011 0.0541 0.1448 85 V 0.5938 0.1349 0.2713 86 D 0.3360 0.1728 0.4911 87 D 0.1388 0.3846 0.4767 88 T 0.1043 0.5663 0.3295 89 L 0.1174 0.6694 0.2132 90 E 0.1061 0.6956 0.1983 91 R 0.1155 0.6663 0.2182 92 A 0.1119 0.5588 0.3294 93 G 0.1103 0.3340 0.5557 94 R 0.1480 0.2724 0.5796 95 I 0.2022 0.2399 0.5579 96 K 0.1259 0.1619 0.7122 97 N 0.0662 0.0548 0.8790