# This file is the result of combining several RDB files, specifically # TR429.t2k.str2.rdb (weight 1.54425) # TR429.t2k.str4.rdb (weight 0.924988) # TR429.t2k.pb.rdb (weight 0.789901) # TR429.t2k.bys.rdb (weight 0.748322) # TR429.t2k.alpha.rdb (weight 0.678173) # 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 TR429.t2k.str2.rdb # ============================================ # TARGET TR429 # Using neural net dunbrack-40pc-3157-t2k-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 TR429.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 5.49968 # # ============================================ # Comments from TR429.t2k.str4.rdb # ============================================ # TARGET TR429 # Using neural net dunbrack-40pc-3157-t2k-IDGaaH13-3-13-7-13-9-13-11-str4-seeded.net # This is a 4-layer network, with # window units # 3 13 # 7 13 # 9 13 # 11 21 (1 str4 ) # The input amino acid frequencies were determined from # alignment TR429.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 5.49968 # # ============================================ # Comments from TR429.t2k.pb.rdb # ============================================ # TARGET TR429 # Using neural net dunbrack-40pc-3157-t2k-IDGaaH13-3-13-7-13-9-13-11-pb-seeded.net # This is a 4-layer network, with # window units # 3 13 # 7 13 # 9 13 # 11 16 (1 pb ) # The input amino acid frequencies were determined from # alignment TR429.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 5.49968 # # ============================================ # Comments from TR429.t2k.bys.rdb # ============================================ # TARGET TR429 # Using neural net dunbrack-40pc-3157-t2k-IDGaaH13-3-13-7-13-9-13-11-bys-seeded.net # This is a 4-layer network, with # window units # 3 13 # 7 13 # 9 13 # 11 11 (1 Bystroff ) # The input amino acid frequencies were determined from # alignment TR429.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 5.49968 # # ============================================ # Comments from TR429.t2k.alpha.rdb # ============================================ # TARGET TR429 # Using neural net dunbrack-40pc-3157-t2k-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 TR429.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 5.49968 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 E 0.2287 0.0891 0.6822 2 T 0.1285 0.2711 0.6005 3 E 0.1720 0.1799 0.6481 4 L 0.3559 0.1217 0.5225 5 G 0.4656 0.0805 0.4539 6 L 0.6351 0.0663 0.2986 7 Y 0.6788 0.0452 0.2760 8 K 0.6605 0.0476 0.2918 9 V 0.4975 0.1051 0.3974 10 N 0.3050 0.1322 0.5628 11 E 0.3084 0.1900 0.5016 12 Y 0.4166 0.1517 0.4317 13 V 0.5402 0.0696 0.3902 14 D 0.3938 0.0518 0.5544 15 A 0.1850 0.4091 0.4059 16 R 0.1511 0.3782 0.4707 17 D 0.1734 0.3010 0.5256 18 T 0.0938 0.4394 0.4668 19 N 0.1031 0.3781 0.5188 20 M 0.1238 0.3128 0.5635 21 G 0.1762 0.2264 0.5974 22 A 0.3263 0.2810 0.3926 23 W 0.5030 0.2147 0.2822 24 F 0.6265 0.1517 0.2218 25 E 0.6459 0.1305 0.2236 26 A 0.7231 0.0669 0.2100 27 Q 0.7219 0.0677 0.2104 28 V 0.6571 0.0691 0.2738 29 V 0.5588 0.1211 0.3201 30 R 0.5838 0.0985 0.3176 31 V 0.4647 0.1434 0.3919 32 T 0.4102 0.1284 0.4615 33 R 0.2986 0.1964 0.5049 34 K 0.2650 0.1445 0.5904 35 A 0.2348 0.0702 0.6949 36 P 0.1557 0.1981 0.6462 37 S 0.1617 0.1719 0.6664 38 R 0.1231 0.2338 0.6431 39 D 0.1371 0.1374 0.7254 40 E 0.2238 0.0692 0.7070 41 P 0.1971 0.1347 0.6682 42 C 0.2404 0.1439 0.6157 43 S 0.1719 0.1804 0.6477 44 S 0.1447 0.2278 0.6275 45 T 0.1349 0.2447 0.6204 46 S 0.1627 0.1570 0.6803 47 R 0.2384 0.0882 0.6733 48 P 0.1998 0.1717 0.6285 49 A 0.2329 0.1779 0.5892 50 L 0.2101 0.2161 0.5738 51 E 0.1774 0.3142 0.5084 52 E 0.1996 0.3033 0.4972 53 D 0.3804 0.1432 0.4764 54 V 0.6156 0.0536 0.3308 55 I 0.7108 0.0242 0.2650 56 Y 0.7855 0.0108 0.2037 57 H 0.7934 0.0069 0.1997 58 V 0.7847 0.0078 0.2075 59 K 0.7300 0.0114 0.2585 60 Y 0.6095 0.0419 0.3486 61 D 0.3396 0.1654 0.4951 62 D 0.2557 0.1732 0.5711 63 Y 0.2491 0.0653 0.6856 64 P 0.1504 0.2326 0.6171 65 E 0.1017 0.3052 0.5931 66 N 0.1549 0.1476 0.6974 67 G 0.2546 0.0858 0.6596 68 V 0.5655 0.0462 0.3882 69 V 0.6808 0.0266 0.2926 70 Q 0.7257 0.0204 0.2539 71 M 0.6649 0.0282 0.3069 72 N 0.3941 0.0290 0.5768 73 S 0.2205 0.2491 0.5304 74 R 0.1296 0.3538 0.5166 75 D 0.1811 0.2249 0.5940 76 V 0.3076 0.1328 0.5596 77 R 0.3645 0.0759 0.5597 78 A 0.2807 0.2607 0.4586 79 R 0.2175 0.2400 0.5425 80 A 0.2024 0.3101 0.4875