# This file is the result of combining several RDB files, specifically # TR432.t04.str2.rdb (weight 1.54425) # TR432.t04.str4.rdb (weight 0.924988) # TR432.t04.pb.rdb (weight 0.789901) # TR432.t04.bys.rdb (weight 0.748322) # TR432.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 TR432.t04.str2.rdb # ============================================ # TARGET TR432 # 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 TR432.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 1442 # # ============================================ # Comments from TR432.t04.str4.rdb # ============================================ # TARGET TR432 # 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 TR432.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 1442 # # ============================================ # Comments from TR432.t04.pb.rdb # ============================================ # TARGET TR432 # 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 TR432.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 1442 # # ============================================ # Comments from TR432.t04.bys.rdb # ============================================ # TARGET TR432 # 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 TR432.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 1442 # # ============================================ # Comments from TR432.t04.alpha.rdb # ============================================ # TARGET TR432 # 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 TR432.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 1442 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 S 0.2032 0.0848 0.7120 2 M 0.1976 0.1791 0.6233 3 Q 0.1635 0.2104 0.6261 4 E 0.1248 0.3480 0.5272 5 E 0.1030 0.3951 0.5019 6 D 0.1059 0.3761 0.5180 7 T 0.1126 0.3497 0.5377 8 F 0.0361 0.7090 0.2549 9 R 0.0129 0.8632 0.1238 10 E 0.0091 0.9087 0.0822 11 L 0.0086 0.9164 0.0751 12 R 0.0083 0.9227 0.0690 13 I 0.0083 0.9235 0.0682 14 F 0.0083 0.9233 0.0684 15 L 0.0083 0.9213 0.0704 16 R 0.0083 0.9226 0.0691 17 N 0.0083 0.9229 0.0688 18 V 0.0083 0.9232 0.0685 19 T 0.0083 0.9204 0.0713 20 H 0.0084 0.9185 0.0731 21 R 0.0089 0.9089 0.0822 22 L 0.0131 0.8819 0.1051 23 A 0.0208 0.8089 0.1703 24 I 0.0449 0.6151 0.3400 25 D 0.1095 0.3578 0.5327 26 K 0.0411 0.5180 0.4409 27 R 0.0740 0.3678 0.5582 28 F 0.2066 0.2416 0.5518 29 R 0.2913 0.1651 0.5436 30 V 0.3059 0.2153 0.4788 31 F 0.3306 0.1852 0.4843 32 T 0.3238 0.1097 0.5666 33 K 0.4469 0.0466 0.5065 34 P 0.3451 0.0432 0.6117 35 V 0.3391 0.0489 0.6120 36 D 0.2010 0.0176 0.7814 37 P 0.0187 0.4882 0.4931 38 D 0.0212 0.6109 0.3679 39 E 0.0674 0.3204 0.6122 40 V 0.1888 0.1248 0.6864 41 P 0.1519 0.2449 0.6032 42 D 0.1488 0.3234 0.5278 43 Y 0.2671 0.3254 0.4074 44 V 0.3608 0.3169 0.3223 45 T 0.4822 0.2508 0.2671 46 V 0.5516 0.1763 0.2721 47 I 0.4421 0.1601 0.3978 48 K 0.3021 0.1468 0.5512 49 Q 0.2640 0.0678 0.6682 50 P 0.2023 0.1199 0.6778 51 M 0.2087 0.1704 0.6209 52 D 0.1972 0.1093 0.6935 53 L 0.0223 0.7072 0.2705 54 S 0.0124 0.8414 0.1462 55 S 0.0151 0.9020 0.0829 56 V 0.0100 0.9172 0.0728 57 I 0.0097 0.9158 0.0745 58 S 0.0108 0.9078 0.0814 59 K 0.0170 0.8701 0.1129 60 I 0.0468 0.8024 0.1508 61 D 0.0386 0.7250 0.2364 62 L 0.0567 0.4438 0.4995 63 H 0.0681 0.2563 0.6755 64 K 0.1609 0.1836 0.6556 65 Y 0.2596 0.1301 0.6103 66 L 0.2698 0.0975 0.6328 67 T 0.2047 0.0266 0.7687 68 V 0.0186 0.7205 0.2609 69 K 0.0105 0.8435 0.1460 70 D 0.0095 0.8901 0.1004 71 Y 0.0099 0.8923 0.0978 72 L 0.0093 0.8932 0.0975 73 R 0.0086 0.8902 0.1011 74 D 0.0098 0.8979 0.0922 75 I 0.0096 0.8952 0.0953 76 D 0.0085 0.9192 0.0723 77 L 0.0093 0.9181 0.0725 78 I 0.0114 0.9092 0.0795 79 C 0.0136 0.8974 0.0890 80 S 0.0147 0.8733 0.1120 81 N 0.0274 0.7750 0.1976 82 A 0.0329 0.7620 0.2051 83 L 0.0559 0.7421 0.2021 84 E 0.1369 0.5802 0.2829 85 Y 0.2254 0.3299 0.4447 86 N 0.2143 0.0888 0.6969 87 P 0.0697 0.3969 0.5334 88 D 0.0665 0.3028 0.6307 89 R 0.0917 0.1832 0.7251 90 D 0.1502 0.0965 0.7533 91 P 0.0511 0.3872 0.5617 92 G 0.0414 0.3139 0.6447 93 D 0.0697 0.4179 0.5124 94 R 0.0791 0.5980 0.3228 95 L 0.1131 0.7299 0.1570 96 I 0.0898 0.8007 0.1095 97 R 0.0219 0.8958 0.0824 98 H 0.0099 0.9159 0.0742 99 R 0.0095 0.9120 0.0784 100 A 0.0084 0.9213 0.0703 101 C 0.0084 0.9222 0.0694 102 A 0.0084 0.9223 0.0694 103 L 0.0084 0.9209 0.0707 104 R 0.0083 0.9224 0.0693 105 D 0.0083 0.9244 0.0673 106 T 0.0083 0.9244 0.0673 107 A 0.0084 0.9222 0.0695 108 Y 0.0083 0.9230 0.0687 109 A 0.0084 0.9234 0.0682 110 I 0.0087 0.9187 0.0726 111 I 0.0095 0.9032 0.0873 112 K 0.0100 0.8801 0.1099 113 E 0.0171 0.8004 0.1825 114 E 0.0595 0.5918 0.3487 115 L 0.0868 0.4118 0.5014 116 D 0.1022 0.3500 0.5479 117 E 0.0411 0.5916 0.3673 118 D 0.0546 0.5805 0.3649 119 F 0.0522 0.6923 0.2555 120 E 0.0519 0.7485 0.1996 121 Q 0.0549 0.7479 0.1972 122 L 0.0776 0.6473 0.2751 123 C 0.0886 0.6365 0.2749 124 E 0.0618 0.7094 0.2288 125 E 0.0859 0.6609 0.2532 126 I 0.1198 0.5768 0.3034 127 Q 0.1127 0.5062 0.3810 128 E 0.1293 0.3613 0.5095 129 S 0.1384 0.2167 0.6450 130 R 0.1393 0.1646 0.6961