# This file is the result of combining several RDB files, specifically # T0487.t2k.str2.rdb (weight 1.54425) # T0487.t2k.str4.rdb (weight 0.924988) # T0487.t2k.pb.rdb (weight 0.789901) # T0487.t2k.bys.rdb (weight 0.748322) # T0487.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 T0487.t2k.str2.rdb # ============================================ # TARGET T0487 # 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 T0487.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 T0487.t2k.str4.rdb # ============================================ # TARGET T0487 # 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 T0487.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 T0487.t2k.pb.rdb # ============================================ # TARGET T0487 # 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 T0487.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 T0487.t2k.bys.rdb # ============================================ # TARGET T0487 # 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 T0487.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 T0487.t2k.alpha.rdb # ============================================ # TARGET T0487 # 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 T0487.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 R 0.2755 0.0302 0.6942 2 P 0.2534 0.0866 0.6599 3 W 0.3409 0.1138 0.5452 4 R 0.5137 0.0737 0.4125 5 L 0.6445 0.0468 0.3087 6 E 0.7092 0.0319 0.2589 7 V 0.7344 0.0207 0.2449 8 V 0.6948 0.0262 0.2790 9 L 0.6046 0.0344 0.3610 10 D 0.3549 0.0249 0.6202 11 P 0.2150 0.0786 0.7063 12 P 0.1895 0.0508 0.7597 13 P 0.1109 0.1979 0.6913 14 G 0.0769 0.1501 0.7729 15 R 0.1274 0.3221 0.5504 16 E 0.1148 0.4969 0.3883 17 E 0.1365 0.4970 0.3665 18 V 0.1313 0.5743 0.2943 19 Y 0.1174 0.6133 0.2693 20 P 0.0329 0.8257 0.1415 21 L 0.0195 0.8677 0.1128 22 L 0.0150 0.8883 0.0967 23 A 0.0140 0.8949 0.0911 24 Q 0.0170 0.8910 0.0919 25 V 0.0265 0.8681 0.1054 26 A 0.0312 0.8425 0.1263 27 R 0.0369 0.7853 0.1778 28 R 0.0739 0.5888 0.3373 29 A 0.0995 0.2760 0.6245 30 G 0.0818 0.1063 0.8119 31 G 0.1934 0.0673 0.7393 32 V 0.4972 0.0376 0.4652 33 T 0.6828 0.0262 0.2911 34 V 0.7251 0.0266 0.2483 35 R 0.6344 0.0369 0.3287 36 M 0.4212 0.0798 0.4990 37 G 0.2331 0.0939 0.6729 38 D 0.1731 0.1463 0.6806 39 G 0.1908 0.1545 0.6547 40 L 0.3217 0.1852 0.4931 41 A 0.3368 0.1917 0.4715 42 S 0.3182 0.1698 0.5120 43 W 0.2642 0.1195 0.6164 44 S 0.2318 0.0441 0.7240 45 P 0.1763 0.0755 0.7482 46 P 0.1377 0.3076 0.5547 47 E 0.2597 0.2824 0.4579 48 V 0.5371 0.1584 0.3046 49 L 0.6466 0.0939 0.2595 50 V 0.6097 0.1367 0.2536 51 L 0.4602 0.1952 0.3446 52 E 0.2786 0.2808 0.4405 53 G 0.1892 0.2754 0.5355 54 T 0.2353 0.4072 0.3574 55 L 0.2022 0.5422 0.2556 56 A 0.1480 0.6256 0.2264 57 R 0.1868 0.5123 0.3010 58 M 0.1532 0.3436 0.5033 59 G 0.1397 0.2143 0.6460 60 Q 0.2355 0.2616 0.5029 61 T 0.3328 0.2532 0.4140 62 Y 0.4050 0.2749 0.3202 63 A 0.4343 0.2757 0.2899 64 Y 0.4902 0.2354 0.2745 65 R 0.5436 0.1567 0.2997 66 L 0.5217 0.1136 0.3647 67 Y 0.3827 0.0543 0.5630 68 P 0.2089 0.1953 0.5959 69 K 0.1203 0.1920 0.6877 70 G 0.0991 0.1433 0.7576 71 R 0.2252 0.0770 0.6978 72 R 0.2948 0.0330 0.6722 73 P 0.2599 0.0631 0.6770 74 L 0.2473 0.1110 0.6417