# 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 5.41598 # # ============================================ # 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 5.41598 # # ============================================ # 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 5.41598 # # ============================================ # 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 5.41598 # # ============================================ # 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 5.41598 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 R 0.2057 0.3587 0.4356 2 A 0.1865 0.5073 0.3062 3 R 0.1940 0.5027 0.3033 4 T 0.3016 0.4116 0.2868 5 I 0.3937 0.2782 0.3280 6 I 0.5004 0.1666 0.3330 7 K 0.3549 0.1569 0.4882 8 W 0.1925 0.3588 0.4487 9 Q 0.1209 0.3886 0.4904 10 D 0.1807 0.2358 0.5835 11 L 0.3178 0.0989 0.5833 12 E 0.2781 0.0943 0.6276 13 V 0.2735 0.1126 0.6139 14 G 0.2607 0.0687 0.6706 15 Q 0.4699 0.0236 0.5065 16 V 0.7389 0.0075 0.2536 17 V 0.8043 0.0068 0.1889 18 M 0.7961 0.0063 0.1976 19 L 0.7730 0.0167 0.2104 20 N 0.6775 0.0211 0.3014 21 Y 0.4206 0.0520 0.5274 22 N 0.2481 0.0256 0.7263 23 P 0.0489 0.4328 0.5183 24 D 0.0711 0.3020 0.6269 25 N 0.1961 0.1085 0.6954 26 P 0.1270 0.3127 0.5603 27 K 0.0979 0.4003 0.5018 28 E 0.1806 0.3636 0.4558 29 R 0.2220 0.1408 0.6372 30 G 0.2546 0.0739 0.6715 31 F 0.5374 0.0400 0.4226 32 W 0.6787 0.0445 0.2768 33 Y 0.6631 0.0538 0.2830 34 D 0.5604 0.0787 0.3610 35 A 0.4129 0.3105 0.2765 36 E 0.4574 0.2991 0.2436 37 I 0.4681 0.3258 0.2061 38 S 0.3699 0.3872 0.2430 39 R 0.3525 0.3732 0.2743 40 K 0.2729 0.3926 0.3345 41 R 0.2490 0.3382 0.4128 42 E 0.2008 0.2803 0.5189 43 T 0.2020 0.1910 0.6070 44 R 0.1891 0.2278 0.5831 45 T 0.2157 0.2306 0.5537 46 A 0.2927 0.1873 0.5200 47 R 0.4279 0.1180 0.4541 48 E 0.5967 0.0540 0.3493 49 L 0.6987 0.0327 0.2686 50 Y 0.7426 0.0218 0.2356 51 A 0.7805 0.0148 0.2046 52 N 0.7594 0.0158 0.2248 53 V 0.7222 0.0253 0.2525 54 V 0.5375 0.0404 0.4221 55 L 0.3043 0.0629 0.6328 56 G 0.1659 0.1102 0.7240 57 D 0.1282 0.2227 0.6492 58 D 0.1361 0.2655 0.5984 59 S 0.2198 0.2354 0.5448 60 L 0.2325 0.2204 0.5470 61 N 0.1976 0.2262 0.5761 62 D 0.1737 0.1732 0.6532 63 C 0.3969 0.0941 0.5090 64 R 0.5752 0.0593 0.3654 65 I 0.6677 0.0494 0.2829 66 I 0.6678 0.0523 0.2799 67 F 0.5515 0.0880 0.3605 68 V 0.2965 0.3617 0.3418 69 D 0.2569 0.4354 0.3077 70 E 0.2841 0.4322 0.2837 71 V 0.4193 0.3169 0.2637 72 F 0.5197 0.2198 0.2606 73 K 0.5617 0.1528 0.2855 74 I 0.5037 0.1259 0.3704 75 E 0.3891 0.0977 0.5132 76 R 0.3264 0.0369 0.6368 77 P 0.2037 0.0760 0.7203