# This file is the result of combining several RDB files, specifically # T0460.t2k.str2.rdb (weight 1.54425) # T0460.t2k.str4.rdb (weight 0.924988) # T0460.t2k.pb.rdb (weight 0.789901) # T0460.t2k.bys.rdb (weight 0.748322) # T0460.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 T0460.t2k.str2.rdb # ============================================ # TARGET T0460 # 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 T0460.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 2.1778 # # ============================================ # Comments from T0460.t2k.str4.rdb # ============================================ # TARGET T0460 # 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 T0460.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 2.1778 # # ============================================ # Comments from T0460.t2k.pb.rdb # ============================================ # TARGET T0460 # 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 T0460.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 2.1778 # # ============================================ # Comments from T0460.t2k.bys.rdb # ============================================ # TARGET T0460 # 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 T0460.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 2.1778 # # ============================================ # Comments from T0460.t2k.alpha.rdb # ============================================ # TARGET T0460 # 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 T0460.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 2.1778 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.1962 0.1606 0.6432 2 N 0.1449 0.1990 0.6561 3 S 0.0257 0.7336 0.2407 4 E 0.0159 0.8385 0.1457 5 V 0.0121 0.9023 0.0856 6 I 0.0091 0.9135 0.0774 7 K 0.0085 0.9140 0.0776 8 E 0.0085 0.9166 0.0750 9 F 0.0095 0.8989 0.0916 10 L 0.0094 0.8744 0.1162 11 E 0.0096 0.8393 0.1511 12 D 0.0209 0.6497 0.3294 13 I 0.0592 0.3497 0.5911 14 G 0.0689 0.2019 0.7292 15 E 0.0898 0.3294 0.5809 16 D 0.1621 0.2458 0.5921 17 Y 0.4821 0.1725 0.3455 18 I 0.6571 0.0578 0.2850 19 E 0.7087 0.0351 0.2562 20 L 0.6314 0.0541 0.3144 21 E 0.4099 0.1111 0.4790 22 N 0.2522 0.1064 0.6414 23 E 0.4823 0.0654 0.4523 24 I 0.6353 0.0442 0.3205 25 H 0.5886 0.0461 0.3653 26 L 0.4733 0.0572 0.4695 27 K 0.3012 0.0414 0.6574 28 P 0.2393 0.2321 0.5286 29 E 0.2757 0.2690 0.4552 30 V 0.4030 0.3084 0.2886 31 F 0.3793 0.4091 0.2116 32 Y 0.5061 0.3228 0.1711 33 E 0.5095 0.3347 0.1557 34 V 0.4487 0.3811 0.1703 35 W 0.3883 0.3999 0.2118 36 K 0.3332 0.3914 0.2753 37 Y 0.3372 0.2589 0.4039 38 V 0.2072 0.1744 0.6185 39 G 0.1394 0.1017 0.7589 40 E 0.2151 0.0609 0.7239 41 P 0.2107 0.2153 0.5740 42 E 0.2778 0.2072 0.5150 43 L 0.4236 0.1455 0.4309 44 K 0.4844 0.0949 0.4207 45 T 0.6521 0.0525 0.2954 46 Y 0.7271 0.0195 0.2534 47 V 0.7365 0.0177 0.2459 48 I 0.6456 0.0340 0.3204 49 E 0.5121 0.0964 0.3915 50 D 0.3863 0.1266 0.4871 51 E 0.4623 0.0989 0.4388 52 I 0.4852 0.0722 0.4426 53 V 0.4596 0.0540 0.4864 54 E 0.3268 0.0356 0.6376 55 P 0.1871 0.1745 0.6384 56 G 0.1282 0.1209 0.7509 57 E 0.2158 0.1357 0.6485 58 Y 0.2831 0.0996 0.6173 59 D 0.2372 0.0502 0.7126 60 P 0.1440 0.1951 0.6609 61 P 0.0696 0.4625 0.4679 62 E 0.1359 0.3842 0.4799 63 M 0.2985 0.2215 0.4800 64 K 0.3637 0.1611 0.4751 65 Y 0.4003 0.1508 0.4490 66 T 0.3201 0.1355 0.5444 67 N 0.3286 0.1225 0.5489 68 V 0.3825 0.1311 0.4864 69 K 0.4612 0.1050 0.4338 70 K 0.6047 0.0574 0.3380 71 V 0.6204 0.0245 0.3550 72 K 0.6764 0.0217 0.3019 73 I 0.6489 0.0289 0.3222 74 K 0.5392 0.0675 0.3933 75 K 0.6845 0.0381 0.2774 76 V 0.6967 0.0261 0.2773 77 Y 0.7557 0.0281 0.2162 78 F 0.7148 0.0403 0.2449 79 E 0.6230 0.0799 0.2971 80 T 0.4952 0.0915 0.4132 81 L 0.3219 0.1616 0.5165 82 D 0.1819 0.1215 0.6966 83 N 0.1120 0.1060 0.7820 84 V 0.3631 0.0363 0.6005 85 R 0.5769 0.0255 0.3976 86 V 0.7200 0.0207 0.2594 87 V 0.6594 0.0430 0.2975 88 T 0.4855 0.0694 0.4451 89 D 0.2423 0.1178 0.6399 90 Y 0.0815 0.4519 0.4666 91 S 0.0289 0.7311 0.2401 92 E 0.0140 0.8579 0.1281 93 F 0.0124 0.8906 0.0970 94 Q 0.0092 0.9176 0.0732 95 K 0.0086 0.9201 0.0713 96 I 0.0091 0.9169 0.0741 97 L 0.0109 0.9058 0.0833 98 K 0.0126 0.8794 0.1080 99 K 0.0252 0.7553 0.2195 100 R 0.0622 0.3194 0.6184 101 G 0.0535 0.1165 0.8300 102 T 0.1724 0.1179 0.7096 103 K 0.2872 0.1481 0.5647 104 L 0.3464 0.2231 0.4305 105 E 0.3134 0.2654 0.4212 106 H 0.2857 0.2576 0.4566 107 H 0.2369 0.2422 0.5209 108 H 0.2116 0.2247 0.5637 109 H 0.1921 0.1955 0.6125 110 H 0.1958 0.1598 0.6443 111 H 0.1874 0.1298 0.6828