# This file is the result of combining several RDB files, specifically # T0576.t2k.str2.rdb (weight 1.54425) # T0576.t2k.str4.rdb (weight 0.924988) # T0576.t2k.pb.rdb (weight 0.789901) # T0576.t2k.bys.rdb (weight 0.748322) # T0576.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 T0576.t2k.str2.rdb # ============================================ # TARGET T0576 # 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 T0576.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 2.06417 # # ============================================ # Comments from T0576.t2k.str4.rdb # ============================================ # TARGET T0576 # 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 T0576.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 2.06417 # # ============================================ # Comments from T0576.t2k.pb.rdb # ============================================ # TARGET T0576 # 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 T0576.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 2.06417 # # ============================================ # Comments from T0576.t2k.bys.rdb # ============================================ # TARGET T0576 # 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 T0576.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 2.06417 # # ============================================ # Comments from T0576.t2k.alpha.rdb # ============================================ # TARGET T0576 # 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 T0576.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 2.06417 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.2248 0.1197 0.6556 2 G 0.1688 0.0970 0.7341 3 S 0.1948 0.1555 0.6497 4 S 0.1920 0.2114 0.5966 5 H 0.2090 0.2323 0.5588 6 H 0.2318 0.2285 0.5397 7 H 0.2446 0.2304 0.5250 8 H 0.2476 0.2089 0.5436 9 H 0.2468 0.1913 0.5619 10 H 0.2068 0.1867 0.6064 11 S 0.1732 0.2208 0.6059 12 S 0.1322 0.1915 0.6763 13 G 0.1221 0.1448 0.7330 14 R 0.2130 0.1974 0.5895 15 E 0.2622 0.2539 0.4839 16 N 0.3504 0.1982 0.4515 17 L 0.4802 0.1433 0.3765 18 Y 0.5308 0.1175 0.3517 19 F 0.5030 0.1056 0.3915 20 Q 0.3483 0.1166 0.5351 21 G 0.2416 0.1094 0.6490 22 H 0.3169 0.0883 0.5947 23 V 0.3412 0.0859 0.5729 24 E 0.2640 0.0513 0.6847 25 P 0.1450 0.1830 0.6720 26 G 0.0992 0.1305 0.7703 27 V 0.2147 0.1927 0.5926 28 T 0.2473 0.2765 0.4762 29 D 0.1644 0.4561 0.3795 30 R 0.1142 0.5638 0.3220 31 I 0.0582 0.6960 0.2458 32 G 0.0280 0.8346 0.1373 33 Q 0.0210 0.8855 0.0935 34 M 0.0219 0.8971 0.0810 35 I 0.0149 0.9098 0.0752 36 L 0.0106 0.9129 0.0765 37 E 0.0134 0.9042 0.0824 38 M 0.0157 0.8764 0.1079 39 F 0.0223 0.8206 0.1572 40 R 0.0487 0.6680 0.2833 41 T 0.0720 0.3967 0.5313 42 G 0.0965 0.2064 0.6971 43 M 0.2790 0.1466 0.5744 44 C 0.4280 0.1174 0.4546 45 L 0.5581 0.1108 0.3311 46 F 0.6616 0.0551 0.2834 47 S 0.6426 0.0467 0.3107 48 V 0.5657 0.0633 0.3710 49 R 0.4488 0.0556 0.4957 50 S 0.2590 0.0448 0.6962 51 P 0.1104 0.2490 0.6407 52 G 0.0908 0.1815 0.7277 53 G 0.1969 0.2625 0.5405 54 V 0.3213 0.3780 0.3007 55 A 0.3718 0.3876 0.2405 56 E 0.3844 0.3783 0.2373 57 L 0.4399 0.2697 0.2904 58 Y 0.3900 0.1853 0.4246 59 G 0.2306 0.1566 0.6128 60 G 0.1838 0.1519 0.6643 61 E 0.3093 0.1494 0.5413 62 A 0.4619 0.1225 0.4156 63 R 0.4695 0.0822 0.4483 64 K 0.6414 0.0414 0.3172 65 V 0.6907 0.0188 0.2905 66 E 0.7149 0.0142 0.2709 67 I 0.6651 0.0248 0.3101 68 T 0.4481 0.0443 0.5077 69 G 0.3525 0.0533 0.5941 70 T 0.4082 0.0646 0.5272 71 S 0.5471 0.0454 0.4075 72 L 0.6053 0.0318 0.3629 73 T 0.6507 0.0238 0.3254 74 I 0.6342 0.0504 0.3154 75 E 0.5775 0.0614 0.3611 76 R 0.4921 0.1148 0.3931 77 E 0.3270 0.2783 0.3946 78 D 0.3673 0.2283 0.4044 79 W 0.4501 0.1903 0.3596 80 H 0.5516 0.1175 0.3309 81 L 0.6271 0.0948 0.2781 82 H 0.6362 0.0771 0.2867 83 C 0.6554 0.0577 0.2869 84 K 0.6046 0.0703 0.3251 85 L 0.5703 0.0996 0.3302 86 E 0.5340 0.1069 0.3591 87 T 0.5743 0.0793 0.3464 88 V 0.5227 0.1052 0.3720 89 E 0.6046 0.0873 0.3081 90 T 0.7201 0.0401 0.2398 91 V 0.7424 0.0288 0.2288 92 V 0.7331 0.0294 0.2375 93 F 0.7162 0.0327 0.2511 94 D 0.5947 0.0398 0.3656 95 L 0.3938 0.0928 0.5134 96 S 0.2601 0.0348 0.7051 97 P 0.1404 0.2306 0.6290 98 K 0.1010 0.2915 0.6076 99 D 0.1185 0.2669 0.6146 100 N 0.1115 0.1430 0.7455 101 G 0.1382 0.1022 0.7596 102 G 0.3801 0.0630 0.5569 103 I 0.6268 0.0354 0.3378 104 R 0.6729 0.0361 0.2910 105 M 0.7940 0.0138 0.1922 106 A 0.7969 0.0089 0.1942 107 V 0.8089 0.0073 0.1838 108 V 0.7890 0.0130 0.1980 109 F 0.6982 0.0310 0.2708 110 R 0.5060 0.1066 0.3875 111 D 0.2806 0.1537 0.5657 112 K 0.0883 0.3550 0.5566 113 H 0.0916 0.3058 0.6026 114 Q 0.1558 0.2360 0.6082 115 A 0.2248 0.1807 0.5944 116 P 0.2171 0.3626 0.4203 117 V 0.2228 0.5454 0.2317 118 L 0.1829 0.6489 0.1683 119 R 0.1065 0.7349 0.1586 120 A 0.0934 0.7266 0.1799 121 A 0.1040 0.6519 0.2441 122 W 0.1526 0.5092 0.3382 123 L 0.2056 0.3619 0.4325 124 P 0.1041 0.5225 0.3734 125 R 0.1139 0.4475 0.4386 126 L 0.1444 0.2917 0.5640 127 M 0.2096 0.1004 0.6900 128 P 0.1376 0.2044 0.6579 129 E 0.1211 0.1775 0.7014 130 T 0.1971 0.0818 0.7211 131 P 0.1553 0.1395 0.7052 132 S 0.2068 0.0555 0.7378 133 P 0.1484 0.0797 0.7719 134 P 0.0443 0.5593 0.3963 135 E 0.0286 0.7175 0.2539 136 Q 0.0488 0.7550 0.1963 137 F 0.0761 0.7654 0.1585 138 W 0.0952 0.7603 0.1445 139 A 0.1201 0.7218 0.1581 140 F 0.1531 0.6281 0.2187 141 T 0.1788 0.5103 0.3109 142 Q 0.2165 0.4551 0.3284 143 R 0.2541 0.3790 0.3669 144 Y 0.3379 0.2392 0.4229 145 I 0.4417 0.1262 0.4321 146 D 0.3776 0.0957 0.5267 147 L 0.3443 0.0620 0.5937 148 P 0.3411 0.1075 0.5514 149 M 0.5349 0.0791 0.3861 150 V 0.6565 0.0485 0.2950 151 V 0.6522 0.0473 0.3005 152 D 0.4376 0.0500 0.5124 153 A 0.2033 0.3599 0.4368 154 R 0.1561 0.3117 0.5321 155 N 0.1851 0.2027 0.6122 156 R 0.2692 0.1802 0.5505 157 Q 0.4705 0.1032 0.4263 158 L 0.5731 0.0553 0.3715 159 V 0.5967 0.0429 0.3604 160 F 0.4513 0.0326 0.5161 161 P 0.2603 0.1152 0.6245 162 G 0.2047 0.0918 0.7034 163 S 0.1982 0.1203 0.6815 164 G 0.1956 0.0962 0.7082 165 Q 0.2096 0.1280 0.6624 166 G 0.1840 0.0998 0.7162 167 G 0.2421 0.1084 0.6495 168 F 0.3056 0.1072 0.5872 169 T 0.2716 0.0995 0.6289 170 E 0.1756 0.1784 0.6460 171 G 0.1392 0.1289 0.7319 172 S 0.1766 0.1166 0.7068