# This file is the result of combining several RDB files, specifically # T0468.t04.str2.rdb (weight 1.54425) # T0468.t04.str4.rdb (weight 0.924988) # T0468.t04.pb.rdb (weight 0.789901) # T0468.t04.bys.rdb (weight 0.748322) # T0468.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 T0468.t04.str2.rdb # ============================================ # TARGET T0468 # 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 T0468.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 42.6786 # # ============================================ # Comments from T0468.t04.str4.rdb # ============================================ # TARGET T0468 # 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 T0468.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 42.6786 # # ============================================ # Comments from T0468.t04.pb.rdb # ============================================ # TARGET T0468 # 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 T0468.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 42.6786 # # ============================================ # Comments from T0468.t04.bys.rdb # ============================================ # TARGET T0468 # 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 T0468.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 42.6786 # # ============================================ # Comments from T0468.t04.alpha.rdb # ============================================ # TARGET T0468 # 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 T0468.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 42.6786 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.2461 0.1220 0.6318 2 E 0.2216 0.1404 0.6380 3 R 0.1943 0.3305 0.4752 4 A 0.1740 0.3947 0.4313 5 S 0.2462 0.3466 0.4072 6 L 0.3148 0.2289 0.4564 7 N 0.3017 0.1640 0.5343 8 R 0.1928 0.2950 0.5122 9 I 0.2162 0.2002 0.5836 10 G 0.2458 0.0946 0.6596 11 K 0.3067 0.0881 0.6053 12 D 0.4252 0.0510 0.5238 13 V 0.6712 0.0142 0.3146 14 Y 0.7769 0.0068 0.2163 15 Y 0.8153 0.0046 0.1801 16 M 0.8240 0.0046 0.1714 17 Q 0.8117 0.0051 0.1833 18 I 0.7710 0.0073 0.2217 19 K 0.5983 0.0330 0.3686 20 G 0.3025 0.0556 0.6419 21 E 0.2096 0.1140 0.6764 22 G 0.2947 0.0779 0.6275 23 T 0.4939 0.0460 0.4601 24 I 0.5680 0.0484 0.3835 25 E 0.5359 0.0786 0.3855 26 K 0.4963 0.1085 0.3952 27 V 0.3907 0.1272 0.4821 28 D 0.2266 0.1114 0.6619 29 G 0.1305 0.1117 0.7578 30 R 0.1984 0.1153 0.6863 31 N 0.4113 0.0544 0.5343 32 L 0.5759 0.0369 0.3872 33 R 0.6877 0.0214 0.2909 34 N 0.7501 0.0129 0.2369 35 Y 0.7666 0.0096 0.2237 36 T 0.7392 0.0106 0.2502 37 L 0.6798 0.0128 0.3074 38 P 0.6338 0.0347 0.3314 39 A 0.6867 0.0430 0.2702 40 Y 0.6709 0.0351 0.2940 41 D 0.3955 0.0231 0.5814 42 E 0.0722 0.3557 0.5721 43 D 0.0745 0.1885 0.7370 44 G 0.1118 0.0935 0.7947 45 V 0.4350 0.0231 0.5420 46 K 0.6485 0.0172 0.3342 47 K 0.7093 0.0199 0.2708 48 Q 0.7770 0.0053 0.2176 49 I 0.7840 0.0072 0.2088 50 T 0.7685 0.0062 0.2253 51 F 0.7539 0.0113 0.2348 52 R 0.6315 0.0370 0.3315 53 S 0.5201 0.0744 0.4055 54 T 0.2993 0.1480 0.5528 55 K 0.2546 0.1541 0.5913 56 K 0.2569 0.1570 0.5861 57 E 0.1755 0.2949 0.5297 58 N 0.1451 0.2796 0.5754 59 D 0.1112 0.3216 0.5672 60 H 0.1673 0.3314 0.5013 61 K 0.2671 0.2338 0.4991 62 L 0.3128 0.1628 0.5243 63 N 0.2516 0.1354 0.6130 64 K 0.1829 0.3102 0.5069 65 Y 0.2461 0.1900 0.5639 66 A 0.5692 0.0587 0.3721 67 F 0.7511 0.0133 0.2356 68 L 0.8053 0.0064 0.1882 69 R 0.8220 0.0051 0.1729 70 L 0.8186 0.0051 0.1763 71 Y 0.7992 0.0078 0.1930 72 V 0.7603 0.0173 0.2224 73 D 0.5928 0.0405 0.3667 74 Q 0.3187 0.1626 0.5187 75 D 0.1976 0.2076 0.5949 76 D 0.1289 0.1832 0.6880 77 N 0.1265 0.1318 0.7416 78 S 0.1998 0.1312 0.6690 79 K 0.2195 0.1871 0.5934 80 N 0.2788 0.1449 0.5763 81 E 0.3250 0.1298 0.5452 82 I 0.3728 0.0960 0.5311 83 S 0.3143 0.1102 0.5755 84 S 0.3480 0.1003 0.5517 85 I 0.4375 0.0488 0.5136 86 E 0.5957 0.0344 0.3699 87 V 0.5831 0.0309 0.3859 88 K 0.5012 0.0380 0.4607 89 S 0.4395 0.0369 0.5236 90 Y 0.2283 0.2882 0.4835 91 E 0.2619 0.4226 0.3155 92 E 0.4468 0.2634 0.2898 93 I 0.4082 0.1927 0.3991 94 Q 0.2298 0.1292 0.6410 95 K 0.0641 0.6243 0.3116 96 A 0.0351 0.6547 0.3101 97 D 0.0556 0.4759 0.4685 98 L 0.1530 0.2250 0.6220 99 P 0.1098 0.3356 0.5545 100 E 0.0136 0.7861 0.2003 101 K 0.0120 0.8467 0.1413 102 V 0.0126 0.8781 0.1093 103 K 0.0126 0.8793 0.1081 104 D 0.0145 0.8400 0.1455 105 K 0.0421 0.6958 0.2621 106 F 0.1202 0.4455 0.4343 107 T 0.1702 0.2438 0.5860 108 I 0.2381 0.1816 0.5804 109 K 0.1783 0.1374 0.6843