# This file is the result of combining several RDB files, specifically # T0316.t2k.dssp-ebghstl.rdb (weight 1.53986) # T0316.t2k.stride-ebghtl.rdb (weight 1.24869) # T0316.t2k.str2.rdb (weight 1.54758) # T0316.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 T0316.t2k.dssp-ebghstl.rdb # ============================================ # TARGET T0316 # 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 T0316.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 336 # # ============================================ # Comments from T0316.t2k.stride-ebghtl.rdb # ============================================ # TARGET T0316 # 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 T0316.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 336 # # ============================================ # Comments from T0316.t2k.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.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 36.379 # # ============================================ # Comments from T0316.t2k.alpha.rdb # ============================================ # TARGET T0316 # 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 T0316.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 336 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 A 0.0885 0.0816 0.8299 2 S 0.1175 0.1368 0.7457 3 Q 0.2398 0.1381 0.6222 4 V 0.4946 0.0563 0.4491 5 H 0.6513 0.0286 0.3201 6 F 0.7535 0.0360 0.2105 7 T 0.6979 0.0364 0.2657 8 R 0.4773 0.0428 0.4800 9 E 0.2285 0.0374 0.7341 10 M 0.1463 0.0308 0.8229 11 P 0.1017 0.0386 0.8597 12 E 0.0681 0.1256 0.8063 13 E 0.0486 0.1225 0.8289 14 F 0.0969 0.0626 0.8405 15 T 0.2181 0.0441 0.7378 16 L 0.5647 0.0174 0.4179 17 E 0.8066 0.0049 0.1884 18 C 0.8809 0.0043 0.1148 19 T 0.9168 0.0032 0.0799 20 A 0.9204 0.0034 0.0762 21 K 0.9197 0.0035 0.0768 22 F 0.9080 0.0033 0.0887 23 R 0.8340 0.0104 0.1556 24 Y 0.7216 0.0139 0.2645 25 R 0.3969 0.0340 0.5690 26 Q 0.1567 0.0274 0.8159 27 P 0.1018 0.0408 0.8574 28 D 0.0935 0.0407 0.8658 29 S 0.1697 0.0146 0.8157 30 K 0.4494 0.0082 0.5424 31 V 0.8329 0.0048 0.1623 32 T 0.9158 0.0034 0.0808 33 V 0.9201 0.0031 0.0768 34 H 0.9063 0.0045 0.0893 35 V 0.8837 0.0047 0.1116 36 K 0.6371 0.0290 0.3339 37 G 0.1190 0.0549 0.8261 38 E 0.0506 0.0590 0.8904 39 K 0.2145 0.0479 0.7376 40 T 0.8111 0.0059 0.1830 41 E 0.9120 0.0035 0.0845 42 V 0.9249 0.0031 0.0720 43 I 0.8854 0.0065 0.1081 44 F 0.7321 0.0079 0.2601 45 A 0.3139 0.0373 0.6488 46 E 0.1863 0.0212 0.7925 47 P 0.2054 0.0647 0.7299 48 Q 0.4526 0.0659 0.4815 49 R 0.6605 0.0552 0.2844 50 A 0.6837 0.0341 0.2821 51 I 0.5852 0.0225 0.3923 52 T 0.2450 0.0220 0.7330 53 P 0.0640 0.0681 0.8679 54 G 0.0799 0.0317 0.8884 55 Q 0.4929 0.0125 0.4946 56 A 0.8424 0.0043 0.1532 57 V 0.9173 0.0038 0.0789 58 V 0.9239 0.0036 0.0726 59 F 0.9172 0.0040 0.0788 60 Y 0.8620 0.0086 0.1294 61 D 0.3049 0.0311 0.6640 62 G 0.0430 0.0530 0.9040 63 E 0.2015 0.0626 0.7359 64 E 0.7650 0.0208 0.2142 65 C 0.8060 0.0329 0.1611 66 L 0.6994 0.0657 0.2349 67 G 0.4780 0.0996 0.4223 68 G 0.3012 0.2785 0.4203 69 G 0.3012 0.4175 0.2814 70 L 0.2569 0.5824 0.1607 71 I 0.1445 0.7502 0.1053 72 D 0.1262 0.7541 0.1197 73 N 0.1553 0.6981 0.1466 74 A 0.1498 0.6554 0.1948 75 Y 0.1800 0.5172 0.3028 76 R 0.1027 0.4245 0.4727 77 D 0.0503 0.1750 0.7746 78 G 0.0434 0.0894 0.8672 79 Q 0.2296 0.0977 0.6726 80 V 0.5910 0.0708 0.3382 81 C 0.5812 0.0913 0.3275 82 Q 0.5820 0.0851 0.3329 83 Y 0.4758 0.0769 0.4473 84 I 0.1781 0.0388 0.7831