# This file is the result of combining several RDB files, specifically # T0487.t04.str2.rdb (weight 1.54425) # T0487.t04.str4.rdb (weight 0.924988) # T0487.t04.pb.rdb (weight 0.789901) # T0487.t04.bys.rdb (weight 0.748322) # T0487.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 T0487.t04.str2.rdb # ============================================ # TARGET T0487 # 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 T0487.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 1 # # ============================================ # Comments from T0487.t04.str4.rdb # ============================================ # TARGET T0487 # 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 T0487.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 1 # # ============================================ # Comments from T0487.t04.pb.rdb # ============================================ # TARGET T0487 # 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 T0487.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 1 # # ============================================ # Comments from T0487.t04.bys.rdb # ============================================ # TARGET T0487 # 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 T0487.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 1 # # ============================================ # Comments from T0487.t04.alpha.rdb # ============================================ # TARGET T0487 # 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 T0487.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 1 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 R 0.2467 0.0433 0.7100 2 P 0.2654 0.1136 0.6209 3 W 0.3689 0.1334 0.4978 4 R 0.5490 0.0756 0.3754 5 L 0.6400 0.0459 0.3141 6 E 0.7018 0.0363 0.2619 7 V 0.7707 0.0142 0.2151 8 V 0.7179 0.0217 0.2604 9 L 0.6279 0.0293 0.3428 10 D 0.3500 0.0239 0.6260 11 P 0.2392 0.0571 0.7037 12 P 0.1949 0.0461 0.7590 13 P 0.1196 0.1780 0.7024 14 G 0.0706 0.1328 0.7966 15 R 0.1113 0.2912 0.5976 16 E 0.0934 0.4728 0.4337 17 E 0.1023 0.5715 0.3263 18 V 0.1168 0.5937 0.2895 19 Y 0.0999 0.6460 0.2541 20 P 0.0255 0.8436 0.1309 21 L 0.0147 0.8795 0.1058 22 L 0.0132 0.8932 0.0937 23 A 0.0096 0.9086 0.0818 24 Q 0.0114 0.9077 0.0809 25 V 0.0126 0.9027 0.0847 26 A 0.0178 0.8744 0.1078 27 R 0.0241 0.8233 0.1526 28 R 0.0613 0.6120 0.3267 29 A 0.1106 0.2916 0.5978 30 G 0.0982 0.1124 0.7893 31 G 0.1957 0.0667 0.7376 32 V 0.5236 0.0338 0.4426 33 T 0.6861 0.0197 0.2942 34 V 0.7262 0.0245 0.2493 35 R 0.6583 0.0329 0.3087 36 M 0.4513 0.0837 0.4649 37 G 0.2392 0.1106 0.6502 38 D 0.1633 0.1584 0.6783 39 G 0.1473 0.1639 0.6889 40 L 0.2346 0.2186 0.5468 41 A 0.2693 0.2279 0.5028 42 S 0.2978 0.1715 0.5307 43 W 0.2682 0.1311 0.6007 44 S 0.2420 0.0478 0.7103 45 P 0.1919 0.0599 0.7482 46 P 0.1731 0.2605 0.5664 47 E 0.2736 0.2130 0.5133 48 V 0.5653 0.1069 0.3279 49 L 0.6640 0.0706 0.2654 50 V 0.7164 0.0518 0.2318 51 L 0.5674 0.1214 0.3113 52 E 0.3443 0.2115 0.4442 53 G 0.2249 0.2441 0.5310 54 T 0.2296 0.4024 0.3680 55 L 0.1740 0.5591 0.2668 56 A 0.1226 0.6440 0.2334 57 R 0.1302 0.5653 0.3045 58 M 0.1443 0.3637 0.4920 59 G 0.1189 0.2420 0.6391 60 Q 0.2049 0.2908 0.5043 61 T 0.3065 0.2913 0.4022 62 Y 0.3333 0.3369 0.3298 63 A 0.3619 0.3218 0.3163 64 Y 0.4534 0.2474 0.2992 65 R 0.5467 0.1522 0.3011 66 L 0.5142 0.1150 0.3707 67 Y 0.3498 0.0562 0.5940 68 P 0.1860 0.2185 0.5955 69 K 0.1180 0.1883 0.6937 70 G 0.0945 0.1346 0.7709 71 R 0.1939 0.0873 0.7188 72 R 0.2799 0.0390 0.6811 73 P 0.2519 0.0747 0.6734 74 L 0.2345 0.1337 0.6318