# This file is the result of combining several RDB files, specifically # TR476.t04.str2.rdb (weight 1.54425) # TR476.t04.str4.rdb (weight 0.924988) # TR476.t04.pb.rdb (weight 0.789901) # TR476.t04.bys.rdb (weight 0.748322) # TR476.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 TR476.t04.str2.rdb # ============================================ # TARGET TR476 # 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 TR476.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 2.29899 # # ============================================ # Comments from TR476.t04.str4.rdb # ============================================ # TARGET TR476 # 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 TR476.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 2.29899 # # ============================================ # Comments from TR476.t04.pb.rdb # ============================================ # TARGET TR476 # 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 TR476.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 2.29899 # # ============================================ # Comments from TR476.t04.bys.rdb # ============================================ # TARGET TR476 # 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 TR476.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 2.29899 # # ============================================ # Comments from TR476.t04.alpha.rdb # ============================================ # TARGET TR476 # 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 TR476.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 2.29899 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 A 0.2539 0.1120 0.6340 2 K 0.2463 0.0996 0.6541 3 C 0.2944 0.0389 0.6668 4 P 0.2572 0.1631 0.5796 5 I 0.2947 0.2005 0.5048 6 C 0.2032 0.1343 0.6625 7 G 0.1309 0.0936 0.7755 8 S 0.1916 0.0572 0.7512 9 P 0.1868 0.1939 0.6194 10 L 0.2226 0.2409 0.5364 11 K 0.1634 0.1615 0.6751 12 W 0.0164 0.7459 0.2377 13 E 0.0092 0.8663 0.1245 14 E 0.0083 0.9198 0.0718 15 L 0.0083 0.9209 0.0708 16 I 0.0084 0.9163 0.0754 17 E 0.0083 0.9161 0.0756 18 E 0.0085 0.9113 0.0802 19 M 0.0103 0.8960 0.0937 20 L 0.0127 0.8666 0.1207 21 I 0.0247 0.8184 0.1570 22 I 0.0357 0.7768 0.1875 23 E 0.0508 0.6662 0.2830 24 N 0.0672 0.5478 0.3850 25 F 0.0215 0.7371 0.2414 26 E 0.0159 0.8315 0.1526 27 E 0.0176 0.8668 0.1156 28 I 0.0296 0.8136 0.1568 29 V 0.0388 0.7565 0.2048 30 K 0.0426 0.6981 0.2594 31 D 0.0829 0.5184 0.3986 32 R 0.0127 0.8250 0.1623 33 E 0.0094 0.8907 0.0999 34 R 0.0091 0.9086 0.0823 35 F 0.0103 0.8939 0.0959 36 L 0.0091 0.8958 0.0951 37 A 0.0097 0.8901 0.1002 38 Q 0.0165 0.8399 0.1436 39 V 0.0230 0.8174 0.1595 40 E 0.0240 0.7728 0.2032 41 E 0.0685 0.6619 0.2697 42 F 0.2259 0.3930 0.3811 43 V 0.3848 0.2281 0.3871 44 F 0.4717 0.1320 0.3962 45 K 0.3767 0.1046 0.5188 46 C 0.2570 0.0429 0.7001 47 P 0.1591 0.2026 0.6383 48 V 0.1694 0.2280 0.6026 49 C 0.1564 0.1878 0.6558 50 G 0.1274 0.2594 0.6132 51 E 0.2026 0.3904 0.4069 52 E 0.2859 0.3852 0.3289 53 F 0.2761 0.3433 0.3806 54 Y 0.1929 0.3005 0.5066 55 G 0.1550 0.2452 0.5998 56 K 0.2227 0.2322 0.5451 57 T 0.2635 0.1288 0.6077 58 L 0.2536 0.0440 0.7024 59 P 0.1659 0.0570 0.7771 60 R 0.0711 0.5012 0.4276 61 R 0.0280 0.7069 0.2650 62 E 0.0229 0.7909 0.1863 63 A 0.0193 0.8567 0.1240 64 E 0.0121 0.8984 0.0895 65 K 0.0168 0.8967 0.0865 66 V 0.0231 0.8909 0.0860 67 F 0.0176 0.9025 0.0798 68 E 0.0207 0.8952 0.0840 69 L 0.0282 0.8623 0.1095 70 L 0.0516 0.7294 0.2190 71 N 0.0524 0.5888 0.3588 72 D 0.0738 0.4156 0.5106 73 F 0.1073 0.3046 0.5881 74 K 0.1220 0.2149 0.6632 75 G 0.1537 0.1525 0.6939 76 G 0.2539 0.1115 0.6347 77 I 0.4103 0.0840 0.5057 78 D 0.3192 0.0506 0.6301 79 W 0.1688 0.3737 0.4576 80 E 0.1264 0.4159 0.4578 81 N 0.2081 0.2015 0.5904 82 K 0.3414 0.1028 0.5559 83 R 0.5541 0.0439 0.4020 84 V 0.7086 0.0145 0.2769 85 K 0.7133 0.0138 0.2730 86 L 0.6925 0.0188 0.2888 87 K 0.4684 0.0448 0.4869