# This file is the result of combining several RDB files, specifically # T0399.t2k.str2.rdb (weight 1.54425) # T0399.t2k.str4.rdb (weight 0.924988) # T0399.t2k.pb.rdb (weight 0.789901) # T0399.t2k.bys.rdb (weight 0.748322) # T0399.t2k.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 T0399.t2k.str2.rdb # ============================================ # TARGET T0399 # Using neural net dunbrack-40pc-3157-t2k-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 T0399.t2k-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 T0399.t2k.str4.rdb # ============================================ # TARGET T0399 # Using neural net dunbrack-40pc-3157-t2k-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 T0399.t2k-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 T0399.t2k.pb.rdb # ============================================ # TARGET T0399 # Using neural net dunbrack-40pc-3157-t2k-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 T0399.t2k-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 T0399.t2k.bys.rdb # ============================================ # TARGET T0399 # Using neural net dunbrack-40pc-3157-t2k-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 T0399.t2k-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 T0399.t2k.alpha.rdb # ============================================ # TARGET T0399 # Using neural net dunbrack-40pc-3157-t2k-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 T0399.t2k-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 M 0.3657 0.1293 0.5050 2 S 0.3049 0.1209 0.5742 3 M 0.2890 0.2774 0.4336 4 K 0.2609 0.2878 0.4513 5 K 0.2636 0.2671 0.4694 6 T 0.2299 0.2199 0.5503 7 K 0.1705 0.3240 0.5055 8 N 0.2153 0.2630 0.5218 9 W 0.4530 0.1947 0.3523 10 L 0.6040 0.1347 0.2612 11 L 0.6863 0.1000 0.2137 12 V 0.6871 0.1153 0.1977 13 F 0.6406 0.1419 0.2176 14 L 0.5550 0.2152 0.2298 15 T 0.4624 0.2924 0.2453 16 V 0.3293 0.4203 0.2505 17 T 0.2954 0.5013 0.2032 18 F 0.2593 0.5773 0.1634 19 C 0.2159 0.6457 0.1384 20 F 0.2403 0.6167 0.1430 21 L 0.2369 0.5870 0.1761 22 M 0.2605 0.4493 0.2902 23 L 0.1906 0.2802 0.5292 24 G 0.1479 0.1519 0.7002 25 C 0.2159 0.1528 0.6314 26 Q 0.2606 0.1573 0.5821 27 S 0.2538 0.1572 0.5890 28 K 0.1402 0.4254 0.4344 29 E 0.1398 0.4434 0.4168 30 D 0.1556 0.3471 0.4973 31 K 0.1511 0.3466 0.5023 32 K 0.1316 0.2231 0.6453 33 G 0.1061 0.1245 0.7694 34 G 0.1519 0.0687 0.7794 35 T 0.2756 0.0564 0.6680 36 K 0.2668 0.0290 0.7042 37 P 0.2118 0.1060 0.6822 38 S 0.1681 0.2376 0.5943 39 N 0.1407 0.3224 0.5369 40 E 0.1251 0.5154 0.3594 41 A 0.1608 0.5439 0.2954 42 A 0.2474 0.4475 0.3050 43 L 0.3176 0.3462 0.3361 44 T 0.3158 0.2508 0.4335 45 K 0.2577 0.2439 0.4984 46 T 0.2134 0.2227 0.5640 47 E 0.1406 0.3086 0.5507 48 N 0.1762 0.2228 0.6010 49 L 0.2771 0.2059 0.5170 50 D 0.3631 0.1664 0.4705 51 F 0.4942 0.1401 0.3658 52 R 0.5742 0.0898 0.3360 53 L 0.6126 0.0774 0.3099 54 S 0.5203 0.0838 0.3959 55 F 0.4246 0.1466 0.4288 56 N 0.3193 0.1385 0.5422 57 K 0.4407 0.0916 0.4677 58 I 0.6033 0.0372 0.3594 59 K 0.6595 0.0246 0.3158 60 V 0.6573 0.0296 0.3131 61 T 0.5030 0.0444 0.4526 62 T 0.3945 0.1014 0.5041 63 D 0.2649 0.1525 0.5826 64 Q 0.1798 0.3435 0.4767 65 N 0.1764 0.2884 0.5352 66 H 0.2332 0.1984 0.5684 67 F 0.2634 0.1374 0.5992 68 S 0.2214 0.1194 0.6593 69 G 0.1643 0.1111 0.7246