# This file is the result of combining several RDB files, specifically # T0397.t06.str2.rdb (weight 1.54425) # T0397.t06.str4.rdb (weight 0.924988) # T0397.t06.pb.rdb (weight 0.789901) # T0397.t06.bys.rdb (weight 0.748322) # T0397.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 T0397.t06.str2.rdb # ============================================ # TARGET T0397 # 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 T0397.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 3.03359 # # ============================================ # Comments from T0397.t06.str4.rdb # ============================================ # TARGET T0397 # 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 T0397.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 3.03359 # # ============================================ # Comments from T0397.t06.pb.rdb # ============================================ # TARGET T0397 # 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 T0397.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 3.03359 # # ============================================ # Comments from T0397.t06.bys.rdb # ============================================ # TARGET T0397 # 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 T0397.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 3.03359 # # ============================================ # Comments from T0397.t06.alpha.rdb # ============================================ # TARGET T0397 # 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 T0397.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 3.03359 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.3663 0.0567 0.5770 2 K 0.3608 0.0413 0.5979 3 I 0.3443 0.0175 0.6382 4 P 0.3865 0.0337 0.5798 5 K 0.7014 0.0193 0.2792 6 I 0.7885 0.0073 0.2042 7 Y 0.7905 0.0074 0.2022 8 V 0.7420 0.0107 0.2473 9 E 0.5395 0.0414 0.4191 10 G 0.3494 0.0385 0.6122 11 E 0.4082 0.0536 0.5382 12 L 0.3774 0.1010 0.5216 13 N 0.2543 0.1246 0.6211 14 D 0.1052 0.1472 0.7476 15 G 0.0777 0.0965 0.8258 16 D 0.3602 0.0322 0.6076 17 R 0.6445 0.0145 0.3410 18 V 0.7711 0.0087 0.2202 19 A 0.7793 0.0072 0.2135 20 I 0.7862 0.0075 0.2063 21 E 0.6875 0.0174 0.2950 22 K 0.5479 0.0603 0.3918 23 D 0.1843 0.0961 0.7196 24 G 0.1268 0.0691 0.8040 25 N 0.3670 0.0392 0.5939 26 A 0.6929 0.0143 0.2928 27 I 0.7813 0.0079 0.2108 28 I 0.7968 0.0092 0.1940 29 F 0.7795 0.0127 0.2078 30 L 0.7045 0.0328 0.2627 31 E 0.5166 0.0570 0.4264 32 K 0.2776 0.1673 0.5551 33 D 0.1893 0.2031 0.6076 34 E 0.1487 0.3611 0.4902 35 E 0.2191 0.3128 0.4681 36 Y 0.2861 0.1866 0.5274 37 S 0.2133 0.1532 0.6334 38 G 0.1272 0.1438 0.7289 39 N 0.1610 0.1027 0.7363 40 G 0.2272 0.0626 0.7102 41 K 0.5984 0.0236 0.3780 42 L 0.7239 0.0136 0.2625 43 L 0.7383 0.0188 0.2429 44 Y 0.8041 0.0112 0.1847 45 Q 0.7923 0.0110 0.1967 46 V 0.7857 0.0119 0.2024 47 I 0.7194 0.0283 0.2522 48 Y 0.4646 0.1778 0.3576 49 D 0.2183 0.3453 0.4363 50 D 0.1269 0.4722 0.4009 51 L 0.0290 0.7691 0.2020 52 A 0.0161 0.8345 0.1494 53 K 0.0193 0.8288 0.1520 54 Y 0.0404 0.7794 0.1801 55 M 0.1098 0.6476 0.2426 56 S 0.1452 0.5357 0.3191 57 L 0.0682 0.6241 0.3077 58 D 0.0558 0.5872 0.3570 59 T 0.1014 0.5586 0.3399 60 L 0.2001 0.4074 0.3926 61 K 0.2225 0.2990 0.4785 62 K 0.3152 0.2484 0.4364 63 D 0.4080 0.1110 0.4810 64 V 0.7160 0.0386 0.2453 65 L 0.7276 0.0236 0.2488 66 I 0.7693 0.0138 0.2169 67 Q 0.7164 0.0195 0.2641 68 Y 0.4618 0.0153 0.5229 69 P 0.1943 0.1530 0.6527 70 D 0.1058 0.1613 0.7328 71 K 0.1780 0.1319 0.6901 72 H 0.3791 0.0753 0.5455 73 T 0.5931 0.0551 0.3518 74 L 0.6589 0.0551 0.2860 75 T 0.6840 0.0722 0.2438 76 Y 0.7040 0.0648 0.2312 77 L 0.5869 0.1437 0.2693 78 K 0.4458 0.2051 0.3491 79 A 0.2341 0.2158 0.5501 80 G 0.1381 0.1195 0.7424 81 T 0.2312 0.0906 0.6782 82 K 0.2225 0.1644 0.6130