# This file is the result of combining several RDB files, specifically # TR429.t06.str2.rdb (weight 1.54425) # TR429.t06.str4.rdb (weight 0.924988) # TR429.t06.pb.rdb (weight 0.789901) # TR429.t06.bys.rdb (weight 0.748322) # TR429.t06.alpha.rdb (weight 0.678173) # TR429.t04.str2.rdb (weight 1.54425) # TR429.t04.str4.rdb (weight 0.924988) # TR429.t04.pb.rdb (weight 0.789901) # TR429.t04.bys.rdb (weight 0.748322) # TR429.t04.alpha.rdb (weight 0.678173) # TR429.t2k.str2.rdb (weight 1.54425) # TR429.t2k.str4.rdb (weight 0.924988) # TR429.t2k.pb.rdb (weight 0.789901) # TR429.t2k.bys.rdb (weight 0.748322) # TR429.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 TR429.t06.str2.rdb # ============================================ # TARGET TR429 # 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 TR429.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 5.80399 # # ============================================ # Comments from TR429.t06.str4.rdb # ============================================ # TARGET TR429 # 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 TR429.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 5.80399 # # ============================================ # Comments from TR429.t06.pb.rdb # ============================================ # TARGET TR429 # 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 TR429.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 5.80399 # # ============================================ # Comments from TR429.t06.bys.rdb # ============================================ # TARGET TR429 # 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 TR429.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 5.80399 # # ============================================ # Comments from TR429.t06.alpha.rdb # ============================================ # TARGET TR429 # 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 TR429.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 5.80399 # # ============================================ # Comments from TR429.t04.str2.rdb # ============================================ # TARGET TR429 # 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 TR429.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 5.85934 # # ============================================ # Comments from TR429.t04.str4.rdb # ============================================ # TARGET TR429 # 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 TR429.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 5.85934 # # ============================================ # Comments from TR429.t04.pb.rdb # ============================================ # TARGET TR429 # 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 TR429.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 5.85934 # # ============================================ # Comments from TR429.t04.bys.rdb # ============================================ # TARGET TR429 # 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 TR429.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 5.85934 # # ============================================ # Comments from TR429.t04.alpha.rdb # ============================================ # TARGET TR429 # 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 TR429.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 5.85934 # # ============================================ # Comments from TR429.t2k.str2.rdb # ============================================ # TARGET TR429 # 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 TR429.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 6.43603 # # ============================================ # Comments from TR429.t2k.str4.rdb # ============================================ # TARGET TR429 # 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 TR429.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 6.43603 # # ============================================ # Comments from TR429.t2k.pb.rdb # ============================================ # TARGET TR429 # 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 TR429.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 6.43603 # # ============================================ # Comments from TR429.t2k.bys.rdb # ============================================ # TARGET TR429 # 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 TR429.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 6.43603 # # ============================================ # Comments from TR429.t2k.alpha.rdb # ============================================ # TARGET TR429 # 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 TR429.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 6.43603 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 E 0.2234 0.0857 0.6909 2 T 0.1125 0.2963 0.5913 3 E 0.1493 0.2040 0.6466 4 L 0.3112 0.1354 0.5533 5 G 0.4193 0.0935 0.4872 6 L 0.6141 0.0701 0.3158 7 Y 0.6669 0.0451 0.2880 8 K 0.6585 0.0445 0.2969 9 V 0.4985 0.1009 0.4007 10 N 0.3079 0.1279 0.5642 11 E 0.3161 0.1860 0.4979 12 Y 0.4192 0.1504 0.4304 13 V 0.5385 0.0700 0.3915 14 D 0.3893 0.0521 0.5586 15 A 0.1832 0.4051 0.4117 16 R 0.1508 0.3732 0.4760 17 D 0.1733 0.2979 0.5288 18 T 0.0942 0.4384 0.4673 19 N 0.1042 0.3776 0.5182 20 M 0.1230 0.3192 0.5577 21 G 0.1760 0.2323 0.5918 22 A 0.3187 0.2933 0.3880 23 W 0.4872 0.2306 0.2822 24 F 0.6123 0.1666 0.2211 25 E 0.6344 0.1429 0.2227 26 A 0.7162 0.0733 0.2105 27 Q 0.7149 0.0755 0.2097 28 V 0.6512 0.0754 0.2734 29 V 0.5523 0.1313 0.3164 30 R 0.5941 0.1064 0.2995 31 V 0.4849 0.1462 0.3689 32 T 0.4395 0.1326 0.4279 33 R 0.3323 0.1846 0.4830 34 K 0.2877 0.1311 0.5811 35 A 0.2365 0.0636 0.6999 36 P 0.1496 0.1991 0.6513 37 S 0.1563 0.1718 0.6719 38 R 0.1246 0.2255 0.6499 39 D 0.1367 0.1434 0.7200 40 E 0.2200 0.0782 0.7018 41 P 0.1994 0.1340 0.6666 42 C 0.2435 0.1269 0.6296 43 S 0.1801 0.1602 0.6597 44 S 0.1460 0.2185 0.6355 45 T 0.1350 0.2370 0.6280 46 S 0.1632 0.1539 0.6829 47 R 0.2358 0.0921 0.6722 48 P 0.2036 0.1794 0.6170 49 A 0.2393 0.1744 0.5863 50 L 0.2131 0.2253 0.5616 51 E 0.1806 0.2964 0.5231 52 E 0.2049 0.2722 0.5229 53 D 0.3844 0.1224 0.4933 54 V 0.6400 0.0384 0.3217 55 I 0.7287 0.0173 0.2540 56 Y 0.7937 0.0088 0.1975 57 H 0.8002 0.0063 0.1935 58 V 0.7916 0.0071 0.2013 59 K 0.7543 0.0096 0.2361 60 Y 0.6515 0.0319 0.3166 61 D 0.4054 0.1329 0.4617 62 D 0.2894 0.1519 0.5587 63 Y 0.2538 0.0573 0.6890 64 P 0.1492 0.2408 0.6100 65 E 0.1056 0.2948 0.5995 66 N 0.1642 0.1486 0.6873 67 G 0.2621 0.0744 0.6636 68 V 0.5645 0.0358 0.3997 69 V 0.6844 0.0232 0.2923 70 Q 0.7284 0.0180 0.2536 71 M 0.6705 0.0247 0.3048 72 N 0.4003 0.0282 0.5715 73 S 0.2156 0.2555 0.5289 74 R 0.1166 0.3536 0.5297 75 D 0.1618 0.2225 0.6157 76 V 0.2613 0.1696 0.5692 77 R 0.3078 0.1381 0.5542 78 A 0.1513 0.5266 0.3220 79 R 0.1364 0.5515 0.3120 80 A 0.1099 0.6663 0.2238 81 R 0.1280 0.6147 0.2573 82 T 0.2425 0.5082 0.2494 83 I 0.3188 0.3540 0.3272 84 I 0.4631 0.1966 0.3403 85 K 0.3353 0.1702 0.4945 86 W 0.1816 0.3764 0.4421 87 Q 0.1193 0.3998 0.4809 88 D 0.1797 0.2394 0.5809 89 L 0.3131 0.0976 0.5893 90 E 0.2757 0.0938 0.6304 91 V 0.2714 0.1127 0.6159 92 G 0.2600 0.0678 0.6722 93 Q 0.4683 0.0227 0.5090 94 V 0.7395 0.0075 0.2530 95 V 0.8038 0.0069 0.1893 96 M 0.7965 0.0063 0.1972 97 L 0.7729 0.0169 0.2101 98 N 0.6791 0.0217 0.2992 99 Y 0.4227 0.0514 0.5259 100 N 0.2491 0.0254 0.7254 101 P 0.0481 0.4412 0.5106 102 D 0.0701 0.3068 0.6232 103 N 0.1970 0.1100 0.6930 104 P 0.1284 0.3152 0.5564 105 K 0.1000 0.4033 0.4967 106 E 0.1879 0.3636 0.4485 107 R 0.2290 0.1382 0.6328 108 G 0.2543 0.0736 0.6721 109 F 0.5319 0.0409 0.4272 110 W 0.6744 0.0472 0.2784 111 Y 0.6534 0.0602 0.2864 112 D 0.5391 0.0924 0.3685 113 A 0.3688 0.3629 0.2683 114 E 0.3954 0.3709 0.2337 115 I 0.3876 0.4143 0.1982 116 S 0.2763 0.4895 0.2342 117 R 0.2266 0.5344 0.2390 118 K 0.1560 0.5858 0.2582 119 R 0.1373 0.5766 0.2861 120 E 0.1181 0.5538 0.3281 121 T 0.1194 0.5645 0.3161 122 R 0.1085 0.6064 0.2851 123 T 0.1182 0.5820 0.2998 124 A 0.0846 0.6507 0.2647 125 R 0.0860 0.6701 0.2439 126 E 0.1472 0.5907 0.2621 127 L 0.2475 0.4741 0.2784 128 Y 0.4158 0.2828 0.3014 129 A 0.5709 0.1565 0.2726 130 N 0.6237 0.1005 0.2758 131 V 0.6583 0.0652 0.2764 132 V 0.5675 0.0537 0.3787 133 L 0.3634 0.0614 0.5752 134 G 0.1943 0.0818 0.7239 135 D 0.1276 0.2150 0.6574 136 D 0.1221 0.2597 0.6182 137 S 0.2042 0.2218 0.5739 138 L 0.2193 0.2177 0.5630 139 N 0.1924 0.2243 0.5833 140 D 0.1719 0.1666 0.6615 141 C 0.3981 0.0872 0.5147 142 R 0.5857 0.0542 0.3601 143 I 0.6710 0.0461 0.2829 144 I 0.6638 0.0510 0.2852 145 F 0.5422 0.0859 0.3719 146 V 0.2861 0.3704 0.3435 147 D 0.2509 0.4437 0.3055 148 E 0.2758 0.4457 0.2785 149 V 0.4049 0.3362 0.2589 150 F 0.5063 0.2365 0.2572 151 K 0.5499 0.1655 0.2845 152 I 0.4953 0.1335 0.3712 153 E 0.3868 0.1019 0.5112 154 R 0.3282 0.0373 0.6345 155 P 0.2055 0.0748 0.7197