# This file is the result of combining several RDB files, specifically # T0409.t04.str2.rdb (weight 1.54425) # T0409.t04.str4.rdb (weight 0.924988) # T0409.t04.pb.rdb (weight 0.789901) # T0409.t04.bys.rdb (weight 0.748322) # T0409.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 T0409.t04.str2.rdb # ============================================ # TARGET T0409 # 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 T0409.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 24.6872 # # ============================================ # Comments from T0409.t04.str4.rdb # ============================================ # TARGET T0409 # 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 T0409.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 24.6872 # # ============================================ # Comments from T0409.t04.pb.rdb # ============================================ # TARGET T0409 # 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 T0409.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 24.6872 # # ============================================ # Comments from T0409.t04.bys.rdb # ============================================ # TARGET T0409 # 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 T0409.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 24.6872 # # ============================================ # Comments from T0409.t04.alpha.rdb # ============================================ # TARGET T0409 # 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 T0409.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 24.6872 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 Y 0.2509 0.1016 0.6475 2 R 0.2813 0.0903 0.6284 3 G 0.1819 0.0459 0.7722 4 P 0.1198 0.3543 0.5259 5 E 0.0650 0.6206 0.3145 6 A 0.0814 0.6210 0.2975 7 F 0.1338 0.4991 0.3671 8 L 0.2255 0.3546 0.4199 9 K 0.2298 0.1761 0.5942 10 L 0.2139 0.0583 0.7278 11 P 0.1600 0.0948 0.7452 12 K 0.0843 0.4197 0.4960 13 D 0.0964 0.3148 0.5889 14 L 0.0558 0.6124 0.3317 15 K 0.0550 0.5408 0.4042 16 D 0.0958 0.5817 0.3225 17 R 0.0120 0.8332 0.1548 18 E 0.0095 0.8933 0.0972 19 A 0.0101 0.9099 0.0800 20 L 0.0087 0.9093 0.0820 21 Q 0.0085 0.9192 0.0722 22 D 0.0084 0.9160 0.0756 23 I 0.0089 0.8973 0.0938 24 M 0.0100 0.8667 0.1233 25 Q 0.0115 0.7622 0.2263 26 D 0.0244 0.5546 0.4210 27 I 0.0926 0.2811 0.6263 28 G 0.0868 0.2473 0.6659 29 N 0.1093 0.2363 0.6544 30 S 0.0793 0.3230 0.5977 31 D 0.0627 0.3253 0.6120 32 D 0.1170 0.2938 0.5892 33 I 0.2719 0.1786 0.5494 34 L 0.4230 0.1544 0.4226 35 A 0.5623 0.1172 0.3205 36 A 0.7283 0.0344 0.2373 37 V 0.7759 0.0178 0.2063 38 V 0.7540 0.0145 0.2315 39 L 0.7345 0.0295 0.2360 40 S 0.6938 0.0224 0.2838 41 A 0.5338 0.0403 0.4259 42 T 0.2452 0.0211 0.7336 43 P 0.0750 0.3011 0.6239 44 G 0.0682 0.2514 0.6804 45 A 0.4172 0.1357 0.4471 46 V 0.6758 0.0432 0.2810 47 E 0.7413 0.0491 0.2097 48 A 0.8023 0.0148 0.1829 49 F 0.7608 0.0314 0.2078 50 R 0.6968 0.0268 0.2764 51 K 0.4798 0.1331 0.3872 52 N 0.1469 0.1011 0.7520 53 G 0.1500 0.0549 0.7951 54 E 0.5061 0.0187 0.4752 55 T 0.7134 0.0084 0.2782 56 I 0.7665 0.0092 0.2243 57 R 0.7789 0.0053 0.2158 58 I 0.7446 0.0114 0.2440 59 T 0.5138 0.0420 0.4442 60 G 0.2110 0.1935 0.5955 61 D 0.0974 0.2651 0.6375 62 G 0.0985 0.2634 0.6381 63 L 0.0883 0.5254 0.3862 64 K 0.0494 0.7711 0.1796 65 A 0.0377 0.8235 0.1388 66 A 0.0297 0.8405 0.1298 67 H 0.0279 0.8512 0.1209 68 R 0.0248 0.8059 0.1693 69 F 0.0409 0.7010 0.2581 70 L 0.0851 0.4872 0.4277 71 S 0.1071 0.2626 0.6303 72 N 0.0915 0.2251 0.6834 73 D 0.1784 0.1036 0.7180 74 P 0.0830 0.3387 0.5784 75 K 0.1171 0.2845 0.5985 76 I 0.1814 0.1585 0.6601 77 G 0.1439 0.1848 0.6713 78 E 0.1711 0.2426 0.5863 79 K 0.3001 0.1604 0.5396 80 R 0.4940 0.0784 0.4276 81 I 0.5118 0.0288 0.4594 82 R 0.3701 0.0180 0.6119 83 P 0.1957 0.1142 0.6901 84 G 0.1899 0.0864 0.7237 85 A 0.6218 0.0157 0.3625 86 L 0.7618 0.0065 0.2317 87 I 0.8115 0.0051 0.1835 88 R 0.8158 0.0046 0.1796 89 V 0.7914 0.0056 0.2031 90 K 0.7734 0.0108 0.2158 91 K 0.7084 0.0202 0.2714 92 T 0.5360 0.0563 0.4076 93 E 0.2077 0.1526 0.6397 94 K 0.1240 0.1318 0.7442 95 G 0.1092 0.0889 0.8019 96 S 0.4044 0.0272 0.5684 97 W 0.6821 0.0162 0.3017 98 Q 0.7609 0.0108 0.2284 99 I 0.7610 0.0147 0.2243 100 V 0.7270 0.0285 0.2445 101 Q 0.6534 0.0229 0.3237 102 L 0.3988 0.0217 0.5795 103 P 0.2460 0.0398 0.7142