# This file is the result of combining several RDB files, specifically # TR462.t04.str2.rdb (weight 1.54425) # TR462.t04.str4.rdb (weight 0.924988) # TR462.t04.pb.rdb (weight 0.789901) # TR462.t04.bys.rdb (weight 0.748322) # TR462.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 TR462.t04.str2.rdb # ============================================ # TARGET TR462 # 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 TR462.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 76.5829 # # ============================================ # Comments from TR462.t04.str4.rdb # ============================================ # TARGET TR462 # 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 TR462.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 76.5829 # # ============================================ # Comments from TR462.t04.pb.rdb # ============================================ # TARGET TR462 # 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 TR462.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 76.5829 # # ============================================ # Comments from TR462.t04.bys.rdb # ============================================ # TARGET TR462 # 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 TR462.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 76.5829 # # ============================================ # Comments from TR462.t04.alpha.rdb # ============================================ # TARGET TR462 # 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 TR462.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 76.5829 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.3614 0.0258 0.6128 2 K 0.2835 0.0209 0.6956 3 L 0.1796 0.3713 0.4492 4 S 0.1254 0.4775 0.3971 5 R 0.1914 0.2947 0.5139 6 L 0.3042 0.0652 0.6306 7 V 0.2513 0.0383 0.7104 8 P 0.1348 0.1198 0.7454 9 G 0.0708 0.0922 0.8370 10 V 0.3256 0.0244 0.6500 11 P 0.5944 0.0206 0.3850 12 A 0.7445 0.0093 0.2462 13 R 0.7790 0.0078 0.2133 14 I 0.7062 0.0050 0.2888 15 K 0.6859 0.0154 0.2987 16 R 0.7605 0.0071 0.2324 17 L 0.6607 0.0185 0.3208 18 E 0.4904 0.0403 0.4693 19 V 0.2883 0.1109 0.6008 20 S 0.1390 0.1996 0.6614 21 G 0.0473 0.4906 0.4621 22 E 0.0317 0.7421 0.2261 23 L 0.0192 0.8592 0.1216 24 H 0.0116 0.8976 0.0908 25 E 0.0094 0.9160 0.0746 26 K 0.0097 0.9123 0.0779 27 L 0.0120 0.8920 0.0961 28 V 0.0149 0.8590 0.1260 29 G 0.0242 0.7015 0.2742 30 M 0.0803 0.3215 0.5982 31 G 0.1110 0.1258 0.7631 32 F 0.2445 0.0642 0.6913 33 V 0.3073 0.0288 0.6640 34 P 0.1500 0.1308 0.7192 35 G 0.0636 0.1101 0.8262 36 E 0.3659 0.0280 0.6061 37 E 0.6608 0.0142 0.3250 38 I 0.7722 0.0082 0.2196 39 E 0.7806 0.0082 0.2112 40 I 0.7542 0.0056 0.2401 41 V 0.7458 0.0221 0.2321 42 Q 0.7463 0.0214 0.2323 43 V 0.6762 0.0372 0.2866 44 A 0.4714 0.0275 0.5011 45 P 0.2956 0.0882 0.6162 46 L 0.1546 0.1312 0.7142 47 G 0.1126 0.0818 0.8056 48 D 0.2406 0.0234 0.7359 49 P 0.4322 0.0622 0.5056 50 I 0.7165 0.0366 0.2468 51 V 0.7986 0.0074 0.1940 52 C 0.8030 0.0066 0.1903 53 K 0.7533 0.0063 0.2404 54 I 0.6615 0.0314 0.3071 55 G 0.3738 0.0590 0.5672 56 N 0.2001 0.0842 0.7157 57 R 0.4731 0.0609 0.4660 58 N 0.6414 0.0524 0.3062 59 I 0.7060 0.0722 0.2218 60 T 0.6841 0.0841 0.2318 61 L 0.6285 0.1169 0.2545 62 R 0.3418 0.2125 0.4457 63 K 0.1184 0.5456 0.3361 64 R 0.0708 0.6422 0.2870 65 E 0.0819 0.5911 0.3270 66 A 0.2436 0.3412 0.4152 67 D 0.2167 0.2646 0.5187 68 L 0.5457 0.0640 0.3903 69 I 0.6342 0.0175 0.3483 70 E 0.7364 0.0118 0.2518 71 V 0.7632 0.0087 0.2281 72 E 0.7161 0.0164 0.2676 73 V 0.6351 0.0194 0.3455 74 V 0.3884 0.0726 0.5390 75 G 0.2159 0.0928 0.6913 76 G 0.1704 0.1189 0.7107 77 E 0.2597 0.1123 0.6280 78 L 0.3623 0.0585 0.5792 79 P 0.3511 0.1061 0.5429 80 L 0.4409 0.1573 0.4018 81 I 0.5278 0.1171 0.3551 82 L 0.5189 0.1060 0.3751 83 A 0.3960 0.1137 0.4903 84 D 0.2596 0.1559 0.5845 85 D 0.1322 0.1296 0.7382 86 G 0.1213 0.0951 0.7836 87 T 0.3511 0.0691 0.5797 88 Y 0.5473 0.0454 0.4074 89 E 0.6193 0.0493 0.3314 90 I 0.6340 0.0447 0.3213 91 T 0.5449 0.0885 0.3666 92 K 0.4722 0.1243 0.4034 93 L 0.3300 0.1961 0.4738 94 N 0.1849 0.1845 0.6307 95 G 0.1209 0.1541 0.7250 96 G 0.1525 0.1810 0.6665 97 R 0.1900 0.3479 0.4621 98 R 0.1925 0.5134 0.2941 99 F 0.1470 0.6501 0.2028 100 L 0.1142 0.7445 0.1413 101 F 0.0872 0.7979 0.1149 102 R 0.0884 0.7856 0.1261 103 M 0.0874 0.7493 0.1633 104 K 0.0724 0.7023 0.2253 105 N 0.1055 0.5067 0.3878 106 L 0.2433 0.2321 0.5246 107 G 0.2894 0.1580 0.5526 108 I 0.3341 0.1281 0.5378 109 E 0.3032 0.1606 0.5362 110 S 0.1405 0.1220 0.7375 111 G 0.0916 0.0842 0.8243 112 K 0.4088 0.0175 0.5737 113 K 0.6929 0.0084 0.2987 114 I 0.7693 0.0084 0.2222 115 Q 0.7750 0.0065 0.2185 116 V 0.7486 0.0078 0.2435 117 S 0.5593 0.0342 0.4065 118 G 0.3349 0.0450 0.6200 119 R 0.2748 0.0495 0.6757 120 R 0.1988 0.2293 0.5719 121 Y 0.2291 0.1840 0.5868 122 Y 0.3346 0.1205 0.5448 123 I 0.3554 0.1269 0.5178 124 E 0.3207 0.1454 0.5339 125 G 0.2729 0.1645 0.5626 126 R 0.3410 0.2420 0.4170 127 E 0.4412 0.2801 0.2787 128 I 0.4957 0.2597 0.2446 129 D 0.4057 0.2692 0.3251 130 L 0.2807 0.3830 0.3363 131 G 0.2205 0.3293 0.4502 132 Y 0.1948 0.2430 0.5622 133 G 0.1720 0.2048 0.6231 134 E 0.1959 0.2982 0.5058 135 A 0.2885 0.1866 0.5249 136 T 0.4303 0.0970 0.4727 137 K 0.6487 0.0268 0.3245 138 I 0.7365 0.0156 0.2479 139 W 0.7528 0.0155 0.2317 140 V 0.7521 0.0169 0.2311 141 R 0.7003 0.0148 0.2849 142 R 0.6371 0.0230 0.3400 143 V 0.4754 0.0415 0.4830