# This file is the result of combining several RDB files, specifically # TR462.t06.str2.rdb (weight 1.54425) # TR462.t06.str4.rdb (weight 0.924988) # TR462.t06.pb.rdb (weight 0.789901) # TR462.t06.bys.rdb (weight 0.748322) # TR462.t06.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 TR462.t06.str2.rdb # ============================================ # TARGET TR462 # Using neural net dunbrack-40pc-3157-t06-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 TR462.t06-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 75.2253 # # ============================================ # Comments from TR462.t06.str4.rdb # ============================================ # TARGET TR462 # Using neural net dunbrack-40pc-3157-t06-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 TR462.t06-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 75.2253 # # ============================================ # Comments from TR462.t06.pb.rdb # ============================================ # TARGET TR462 # Using neural net dunbrack-40pc-3157-t06-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 TR462.t06-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 75.2253 # # ============================================ # Comments from TR462.t06.bys.rdb # ============================================ # TARGET TR462 # Using neural net dunbrack-40pc-3157-t06-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 TR462.t06-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 75.2253 # # ============================================ # Comments from TR462.t06.alpha.rdb # ============================================ # TARGET TR462 # Using neural net dunbrack-40pc-3157-t06-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 TR462.t06-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 75.2253 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.3836 0.0275 0.5889 2 K 0.2843 0.0257 0.6900 3 L 0.1858 0.3677 0.4465 4 S 0.1246 0.4874 0.3880 5 R 0.1688 0.3713 0.4600 6 L 0.3086 0.0817 0.6097 7 V 0.2181 0.0370 0.7449 8 P 0.1169 0.1894 0.6938 9 G 0.0442 0.1049 0.8509 10 V 0.2612 0.0221 0.7167 11 P 0.5199 0.0227 0.4574 12 A 0.7396 0.0112 0.2492 13 R 0.7930 0.0074 0.1996 14 I 0.7231 0.0074 0.2695 15 K 0.6707 0.0232 0.3062 16 R 0.7317 0.0147 0.2536 17 L 0.6522 0.0207 0.3271 18 E 0.5122 0.0415 0.4462 19 V 0.3315 0.1114 0.5571 20 S 0.1215 0.2353 0.6432 21 G 0.0437 0.4513 0.5050 22 E 0.0352 0.7403 0.2245 23 L 0.0234 0.8524 0.1242 24 H 0.0111 0.9013 0.0877 25 E 0.0089 0.9151 0.0760 26 K 0.0088 0.9122 0.0790 27 L 0.0112 0.8986 0.0902 28 V 0.0173 0.8556 0.1271 29 G 0.0319 0.6540 0.3141 30 M 0.0854 0.2628 0.6518 31 G 0.1251 0.1109 0.7640 32 F 0.3250 0.0502 0.6248 33 V 0.3065 0.0297 0.6637 34 P 0.1585 0.1334 0.7081 35 G 0.0765 0.0930 0.8305 36 E 0.3594 0.0308 0.6098 37 E 0.6483 0.0153 0.3364 38 I 0.7590 0.0089 0.2321 39 E 0.7727 0.0091 0.2182 40 I 0.7523 0.0076 0.2400 41 V 0.7469 0.0196 0.2335 42 Q 0.7427 0.0199 0.2375 43 V 0.6505 0.0375 0.3120 44 A 0.4181 0.0263 0.5556 45 P 0.2773 0.1212 0.6015 46 L 0.1333 0.1623 0.7044 47 G 0.0901 0.0841 0.8258 48 D 0.2366 0.0232 0.7403 49 P 0.4123 0.0320 0.5558 50 I 0.7145 0.0260 0.2595 51 V 0.7911 0.0070 0.2019 52 C 0.8032 0.0068 0.1900 53 K 0.7733 0.0063 0.2204 54 I 0.6585 0.0184 0.3231 55 G 0.3279 0.0527 0.6195 56 N 0.2402 0.0658 0.6940 57 R 0.5019 0.0476 0.4505 58 N 0.6558 0.0572 0.2870 59 I 0.6949 0.0668 0.2383 60 T 0.6808 0.0889 0.2303 61 L 0.6088 0.1223 0.2689 62 R 0.4006 0.1703 0.4291 63 K 0.1390 0.5335 0.3275 64 R 0.0776 0.6144 0.3080 65 E 0.0839 0.5665 0.3497 66 A 0.1631 0.4831 0.3538 67 D 0.1847 0.3794 0.4359 68 L 0.4460 0.1527 0.4013 69 I 0.6616 0.0310 0.3074 70 E 0.6932 0.0215 0.2853 71 V 0.7350 0.0162 0.2488 72 E 0.7027 0.0260 0.2713 73 V 0.6373 0.0309 0.3317 74 V 0.4691 0.0655 0.4654 75 G 0.2712 0.0596 0.6693