# This file is the result of combining several RDB files, specifically # TR462.t04.str2.rdb (weight 1.54425) # TR462.t04.str4.rdb (weight 0.924988) # TR462.t04.pb.rdb (weight 0.789901) # TR462.t04.bys.rdb (weight 0.748322) # TR462.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 TR462.t04.str2.rdb # ============================================ # TARGET TR462 # 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 TR462.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 68.6508 # # ============================================ # Comments from TR462.t04.str4.rdb # ============================================ # TARGET TR462 # 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 TR462.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 68.6508 # # ============================================ # Comments from TR462.t04.pb.rdb # ============================================ # TARGET TR462 # 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 TR462.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 68.6508 # # ============================================ # Comments from TR462.t04.bys.rdb # ============================================ # TARGET TR462 # 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 TR462.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 68.6508 # # ============================================ # Comments from TR462.t04.alpha.rdb # ============================================ # TARGET TR462 # 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 TR462.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 68.6508 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.3776 0.0256 0.5968 2 K 0.2948 0.0219 0.6833 3 L 0.1981 0.3510 0.4509 4 S 0.1364 0.4478 0.4158 5 R 0.1916 0.2746 0.5337 6 L 0.2983 0.0613 0.6403 7 V 0.2409 0.0368 0.7223 8 P 0.1289 0.1240 0.7470 9 G 0.0647 0.0962 0.8391 10 V 0.3148 0.0237 0.6614 11 P 0.5902 0.0192 0.3906 12 A 0.7466 0.0093 0.2441 13 R 0.7852 0.0073 0.2075 14 I 0.7145 0.0051 0.2804 15 K 0.6853 0.0170 0.2977 16 R 0.7353 0.0097 0.2549 17 L 0.6199 0.0218 0.3583 18 E 0.4506 0.0437 0.5057 19 V 0.2717 0.1313 0.5970 20 S 0.1356 0.2055 0.6588 21 G 0.0453 0.4833 0.4714 22 E 0.0331 0.7396 0.2273 23 L 0.0199 0.8620 0.1181 24 H 0.0111 0.9016 0.0873 25 E 0.0095 0.9152 0.0753 26 K 0.0102 0.9099 0.0799 27 L 0.0111 0.8937 0.0952 28 V 0.0134 0.8657 0.1209 29 G 0.0227 0.7117 0.2656 30 M 0.0759 0.3297 0.5944 31 G 0.1004 0.1269 0.7727 32 F 0.2315 0.0681 0.7004 33 V 0.2867 0.0293 0.6840 34 P 0.1399 0.1341 0.7260 35 G 0.0606 0.1101 0.8294 36 E 0.3462 0.0264 0.6274 37 E 0.6513 0.0142 0.3345 38 I 0.7709 0.0079 0.2212 39 E 0.7779 0.0082 0.2139 40 I 0.7467 0.0056 0.2477 41 V 0.7365 0.0222 0.2413 42 Q 0.7348 0.0204 0.2448 43 V 0.6543 0.0360 0.3096 44 A 0.4376 0.0273 0.5351 45 P 0.2845 0.1013 0.6142 46 L 0.1512 0.1291 0.7197 47 G 0.1160 0.0756 0.8084 48 D 0.2514 0.0215 0.7271 49 P 0.4515 0.0526 0.4960 50 I 0.7202 0.0301 0.2497 51 V 0.8061 0.0060 0.1879 52 C 0.8064 0.0059 0.1878 53 K 0.7592 0.0059 0.2349 54 I 0.6635 0.0299 0.3066 55 G 0.3548 0.0619 0.5833 56 N 0.1891 0.0932 0.7177 57 R 0.4371 0.0825 0.4804 58 N 0.6017 0.0850 0.3132 59 I 0.6406 0.1346 0.2248 60 T 0.6170 0.1570 0.2260 61 L 0.5773 0.1819 0.2408 62 R 0.3176 0.2760 0.4064 63 K 0.1075 0.5756 0.3169 64 R 0.0637 0.6649 0.2714 65 E 0.0758 0.6109 0.3133 66 A 0.2286 0.3855 0.3859 67 D 0.2083 0.3106 0.4811 68 L 0.5505 0.0767 0.3728 69 I 0.6391 0.0225 0.3383 70 E 0.7332 0.0152 0.2516 71 V 0.7527 0.0125 0.2348 72 E 0.7013 0.0189 0.2798 73 V 0.6196 0.0222 0.3583 74 V 0.3641 0.0585 0.5774 75 G 0.2149 0.0652 0.7199