# This file is the result of combining several RDB files, specifically # T0464.t04.str2.rdb (weight 1.54425) # T0464.t04.str4.rdb (weight 0.924988) # T0464.t04.pb.rdb (weight 0.789901) # T0464.t04.bys.rdb (weight 0.748322) # T0464.t04.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 T0464.t04.str2.rdb # ============================================ # TARGET T0464 # Using neural net dunbrack-40pc-3157-t04-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 T0464.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 5.24702 # # ============================================ # Comments from T0464.t04.str4.rdb # ============================================ # TARGET T0464 # Using neural net dunbrack-40pc-3157-t04-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 T0464.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 5.24702 # # ============================================ # Comments from T0464.t04.pb.rdb # ============================================ # TARGET T0464 # Using neural net dunbrack-40pc-3157-t04-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 T0464.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 5.24702 # # ============================================ # Comments from T0464.t04.bys.rdb # ============================================ # TARGET T0464 # Using neural net dunbrack-40pc-3157-t04-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 T0464.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 5.24702 # # ============================================ # Comments from T0464.t04.alpha.rdb # ============================================ # TARGET T0464 # Using neural net dunbrack-40pc-3157-t04-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 T0464.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 5.24702 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.2029 0.1632 0.6339 2 D 0.1654 0.1587 0.6759 3 R 0.0154 0.7300 0.2546 4 K 0.0141 0.8079 0.1780 5 L 0.0219 0.8366 0.1415 6 L 0.0365 0.8137 0.1499 7 H 0.0505 0.7784 0.1711 8 L 0.0947 0.7006 0.2047 9 L 0.1904 0.4859 0.3237 10 C 0.2803 0.2437 0.4760 11 S 0.2113 0.0788 0.7099 12 P 0.0666 0.3301 0.6033 13 D 0.0676 0.2939 0.6385 14 T 0.1079 0.1935 0.6986 15 R 0.1531 0.1440 0.7029 16 Q 0.2931 0.0560 0.6509 17 P 0.3605 0.0711 0.5684 18 L 0.4239 0.1002 0.4759 19 S 0.3686 0.1399 0.4916 20 L 0.2004 0.4569 0.3427 21 L 0.1585 0.5405 0.3010 22 E 0.0959 0.6083 0.2958 23 S 0.0373 0.7285 0.2341 24 K 0.0235 0.7557 0.2208 25 G 0.0253 0.7783 0.1964 26 L 0.0135 0.8551 0.1315 27 E 0.0098 0.9089 0.0813 28 A 0.0091 0.9139 0.0770 29 L 0.0110 0.8987 0.0902 30 N 0.0102 0.8862 0.1036 31 K 0.0085 0.8910 0.1005 32 A 0.0104 0.8828 0.1068 33 I 0.0225 0.8086 0.1689 34 A 0.0346 0.6739 0.2916 35 S 0.0737 0.3099 0.6164 36 G 0.1004 0.1732 0.7264 37 T 0.2665 0.1624 0.5711 38 V 0.4345 0.1726 0.3929 39 Q 0.4624 0.1617 0.3759 40 R 0.4048 0.1497 0.4455 41 A 0.2318 0.2481 0.5201 42 D 0.1219 0.1472 0.7309 43 G 0.0781 0.1079 0.8141 44 S 0.2594 0.0696 0.6710 45 I 0.4181 0.1061 0.4758 46 Q 0.3522 0.1674 0.4804 47 N 0.3239 0.1671 0.5090 48 Q 0.3388 0.1448 0.5164 49 S 0.3143 0.1965 0.4893 50 L 0.2068 0.3938 0.3994 51 H 0.1728 0.4172 0.4100 52 E 0.2333 0.3631 0.4035 53 A 0.3812 0.2344 0.3844 54 L 0.5282 0.1574 0.3143 55 I 0.5945 0.0873 0.3182 56 T 0.4088 0.0780 0.5132 57 R 0.2760 0.1780 0.5460 58 D 0.1836 0.1748 0.6416 59 R 0.1071 0.3214 0.5715 60 K 0.1897 0.2547 0.5556 61 Q 0.4481 0.1307 0.4213 62 V 0.6238 0.0417 0.3345 63 F 0.7008 0.0181 0.2810 64 R 0.6710 0.0165 0.3125 65 I 0.4552 0.0670 0.4779 66 E 0.2310 0.1907 0.5783 67 D 0.1324 0.1297 0.7379 68 S 0.1305 0.0925 0.7770 69 I 0.3349 0.0294 0.6357 70 P 0.5360 0.0269 0.4372 71 V 0.6725 0.0244 0.3031 72 L 0.6325 0.0230 0.3445 73 L 0.3566 0.0258 0.6175 74 P 0.1395 0.3527 0.5078 75 E 0.0396 0.6757 0.2847 76 E 0.0331 0.7187 0.2482 77 A 0.0536 0.7365 0.2099 78 I 0.0823 0.7043 0.2134 79 A 0.0746 0.7004 0.2250 80 T 0.0619 0.7264 0.2118 81 I 0.0783 0.7156 0.2061 82 Q 0.0787 0.7071 0.2143 83 I 0.0950 0.6089 0.2961 84 A 0.1109 0.4338 0.4553 85 N 0.1183 0.2355 0.6461 86 F 0.1928 0.0785 0.7287 87 P 0.1169 0.2795 0.6036 88 D 0.0937 0.2990 0.6073 89 K 0.1187 0.2546 0.6267