# This file is the result of combining several RDB files, specifically # T0417.t06.str2.rdb (weight 1.54425) # T0417.t06.str4.rdb (weight 0.924988) # T0417.t06.pb.rdb (weight 0.789901) # T0417.t06.bys.rdb (weight 0.748322) # T0417.t06.alpha.rdb (weight 0.678173) # T0417.t04.str2.rdb (weight 1.54425) # T0417.t04.str4.rdb (weight 0.924988) # T0417.t04.pb.rdb (weight 0.789901) # T0417.t04.bys.rdb (weight 0.748322) # T0417.t04.alpha.rdb (weight 0.678173) # T0417.t2k.str2.rdb (weight 1.54425) # T0417.t2k.str4.rdb (weight 0.924988) # T0417.t2k.pb.rdb (weight 0.789901) # T0417.t2k.bys.rdb (weight 0.748322) # T0417.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 T0417.t06.str2.rdb # ============================================ # TARGET T0417 # 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 T0417.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 5114 # # ============================================ # Comments from T0417.t06.str4.rdb # ============================================ # TARGET T0417 # 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 T0417.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 5114 # # ============================================ # Comments from T0417.t06.pb.rdb # ============================================ # TARGET T0417 # 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 T0417.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 5114 # # ============================================ # Comments from T0417.t06.bys.rdb # ============================================ # TARGET T0417 # 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 T0417.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 5114 # # ============================================ # Comments from T0417.t06.alpha.rdb # ============================================ # TARGET T0417 # 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 T0417.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 5114 # # ============================================ # Comments from T0417.t04.str2.rdb # ============================================ # TARGET T0417 # 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 T0417.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 2010 # # ============================================ # Comments from T0417.t04.str4.rdb # ============================================ # TARGET T0417 # 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 T0417.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 2010 # # ============================================ # Comments from T0417.t04.pb.rdb # ============================================ # TARGET T0417 # 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 T0417.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 2010 # # ============================================ # Comments from T0417.t04.bys.rdb # ============================================ # TARGET T0417 # 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 T0417.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 2010 # # ============================================ # Comments from T0417.t04.alpha.rdb # ============================================ # TARGET T0417 # 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 T0417.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 2010 # # ============================================ # Comments from T0417.t2k.str2.rdb # ============================================ # TARGET T0417 # 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 T0417.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 275 # # ============================================ # Comments from T0417.t2k.str4.rdb # ============================================ # TARGET T0417 # 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 T0417.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 275 # # ============================================ # Comments from T0417.t2k.pb.rdb # ============================================ # TARGET T0417 # 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 T0417.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 275 # # ============================================ # Comments from T0417.t2k.bys.rdb # ============================================ # TARGET T0417 # 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 T0417.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 275 # # ============================================ # Comments from T0417.t2k.alpha.rdb # ============================================ # TARGET T0417 # 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 T0417.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 275 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 S 0.1725 0.1793 0.6482 2 N 0.1556 0.1983 0.6461 3 A 0.1145 0.3698 0.5157 4 M 0.1650 0.2126 0.6223 5 R 0.1708 0.1620 0.6672 6 K 0.0953 0.3232 0.5815 7 D 0.0976 0.3491 0.5533 8 E 0.0940 0.3849 0.5212 9 T 0.1495 0.2262 0.6243 10 S 0.1302 0.2342 0.6356 11 N 0.1578 0.1660 0.6763 12 T 0.2014 0.1079 0.6907 13 S 0.1938 0.0620 0.7443 14 P 0.1078 0.2760 0.6162 15 D 0.1579 0.2570 0.5851 16 I 0.2529 0.2365 0.5106 17 S 0.2568 0.2328 0.5104 18 V 0.2389 0.3080 0.4531 19 A 0.2979 0.1766 0.5255 20 Q 0.3190 0.0617 0.6193 21 P 0.2240 0.1359 0.6400 22 A 0.1295 0.3281 0.5424 23 S 0.1370 0.3195 0.5435 24 A 0.1837 0.2456 0.5707 25 L 0.2487 0.1646 0.5867 26 R 0.3844 0.0796 0.5360 27 Y 0.5730 0.0299 0.3971 28 H 0.6920 0.0182 0.2897 29 L 0.6442 0.0215 0.3343 30 R 0.4580 0.0177 0.5243 31 P 0.3047 0.0295 0.6658 32 P 0.2580 0.0577 0.6843 33 R 0.1999 0.0340 0.7661 34 R 0.0617 0.4545 0.4838 35 N 0.0537 0.4620 0.4843 36 D 0.0640 0.4352 0.5009 37 G 0.0231 0.7771 0.1998 38 A 0.0124 0.8880 0.0995 39 A 0.0107 0.9095 0.0798 40 I 0.0087 0.9143 0.0770 41 H 0.0084 0.9205 0.0712 42 Q 0.0083 0.9217 0.0700 43 L 0.0086 0.9120 0.0794 44 V 0.0092 0.8746 0.1163 45 S 0.0117 0.7525 0.2358 46 E 0.0318 0.4116 0.5566 47 C 0.1520 0.1249 0.7231 48 P 0.1350 0.1420 0.7230 49 P 0.1175 0.2643 0.6181 50 L 0.1205 0.3084 0.5712 51 D 0.1447 0.2585 0.5969 52 L 0.0818 0.4373 0.4808 53 N 0.0869 0.4188 0.4943 54 S 0.0495 0.6681 0.2824 55 L 0.0226 0.8123 0.1652 56 Y 0.0238 0.8566 0.1197 57 A 0.0201 0.8896 0.0903 58 Y 0.0190 0.8941 0.0869 59 L 0.0208 0.8917 0.0875 60 L 0.0273 0.8672 0.1055 61 L 0.0491 0.7812 0.1697 62 C 0.0644 0.6870 0.2486 63 E 0.0727 0.5513 0.3760 64 H 0.1095 0.3400 0.5505 65 H 0.1624 0.2426 0.5951 66 A 0.1927 0.2495 0.5578 67 H 0.3065 0.1412 0.5523 68 T 0.5993 0.0472 0.3535 69 C 0.7405 0.0128 0.2467 70 V 0.8042 0.0071 0.1886 71 V 0.8066 0.0074 0.1860 72 A 0.7634 0.0118 0.2247 73 E 0.7229 0.0125 0.2646 74 S 0.5540 0.0112 0.4349 75 P 0.2155 0.1279 0.6566 76 G 0.0601 0.1246 0.8153 77 G 0.1271 0.0681 0.8048 78 R 0.4479 0.0197 0.5324 79 I 0.6646 0.0224 0.3130 80 D 0.6458 0.0363 0.3179 81 G 0.7668 0.0173 0.2159 82 F 0.7809 0.0128 0.2063 83 V 0.7895 0.0165 0.1940 84 S 0.7597 0.0307 0.2096 85 A 0.7193 0.0448 0.2359 86 Y 0.6616 0.0445 0.2939 87 L 0.5575 0.0431 0.3994 88 L 0.2941 0.0327 0.6732 89 P 0.1315 0.2094 0.6591 90 T 0.1121 0.1892 0.6987 91 R 0.1821 0.0764 0.7415 92 P 0.1164 0.2569 0.6268 93 D 0.1339 0.2242 0.6420 94 V 0.3964 0.1595 0.4441 95 L 0.6175 0.0765 0.3061 96 F 0.7445 0.0503 0.2051 97 V 0.7402 0.0521 0.2078 98 W 0.7107 0.0734 0.2159 99 Q 0.6660 0.1132 0.2207 100 V 0.6550 0.1117 0.2333 101 A 0.6402 0.0885 0.2714 102 V 0.5918 0.0811 0.3271 103 H 0.3431 0.0669 0.5900 104 S 0.0661 0.5190 0.4150 105 R 0.0451 0.5069 0.4480 106 A 0.0823 0.4948 0.4229 107 R 0.0947 0.3415 0.5637 108 G 0.0741 0.3468 0.5791 109 H 0.0654 0.6262 0.3084 110 R 0.0494 0.7346 0.2160 111 L 0.0209 0.8609 0.1182 112 G 0.0109 0.9118 0.0772 113 R 0.0083 0.9216 0.0700 114 A 0.0083 0.9240 0.0677 115 M 0.0083 0.9225 0.0692 116 L 0.0084 0.9174 0.0742 117 G 0.0083 0.9213 0.0703 118 H 0.0083 0.9201 0.0716 119 I 0.0084 0.9185 0.0731 120 L 0.0084 0.9139 0.0777 121 E 0.0084 0.9109 0.0807 122 R 0.0091 0.8971 0.0938 123 Q 0.0101 0.8768 0.1131 124 E 0.0111 0.8110 0.1779 125 C 0.0220 0.7090 0.2690 126 R 0.0533 0.3282 0.6184 127 H 0.0769 0.1341 0.7890 128 V 0.2718 0.0947 0.6335 129 R 0.4345 0.0927 0.4729 130 H 0.7084 0.0392 0.2524 131 L 0.7111 0.0238 0.2651 132 E 0.7668 0.0146 0.2185 133 T 0.7587 0.0161 0.2252 134 T 0.7353 0.0166 0.2481 135 V 0.5938 0.0278 0.3784 136 G 0.2403 0.0283 0.7314 137 P 0.0671 0.3340 0.5988 138 D 0.0619 0.3131 0.6250 139 N 0.0934 0.3899 0.5167 140 Q 0.0178 0.7564 0.2258 141 A 0.0112 0.8678 0.1210 142 S 0.0094 0.9128 0.0778 143 R 0.0084 0.9190 0.0726 144 R 0.0084 0.9195 0.0722 145 T 0.0084 0.9176 0.0740 146 F 0.0088 0.9084 0.0828 147 A 0.0097 0.8849 0.1054 148 G 0.0142 0.8206 0.1653 149 L 0.0400 0.6707 0.2893 150 A 0.0622 0.4652 0.4726 151 G 0.0932 0.3897 0.5171 152 E 0.1678 0.3425 0.4896 153 R 0.1689 0.1998 0.6313 154 G 0.1382 0.1030 0.7588 155 A 0.2564 0.0885 0.6551 156 H 0.3587 0.0860 0.5554 157 V 0.4247 0.1031 0.4722 158 S 0.3813 0.1162 0.5025 159 E 0.3692 0.1297 0.5011 160 Q 0.3527 0.0545 0.5928 161 P 0.2876 0.1484 0.5639 162 F 0.3139 0.1574 0.5287 163 F 0.3698 0.0917 0.5384 164 D 0.2767 0.1068 0.6165 165 R 0.1307 0.5007 0.3686 166 Q 0.1078 0.5327 0.3595 167 A 0.1786 0.3347 0.4868 168 F 0.1797 0.1533 0.6670 169 G 0.1190 0.1324 0.7485 170 G 0.0940 0.1607 0.7454 171 A 0.1261 0.1693 0.7046 172 D 0.1636 0.1460 0.6904 173 H 0.1972 0.1274 0.6754 174 D 0.1421 0.2937 0.5642 175 D 0.1381 0.4500 0.4119 176 E 0.1983 0.4627 0.3391 177 M 0.3027 0.3671 0.3303 178 L 0.4586 0.2431 0.2983 179 L 0.5781 0.1288 0.2931 180 R 0.6455 0.0550 0.2995 181 I 0.5461 0.0562 0.3976 182 G 0.3599 0.0445 0.5956 183 P 0.3066 0.1107 0.5827 184 F 0.3279 0.0994 0.5727 185 T 0.2958 0.0735 0.6307 186 H 0.2597 0.0400 0.7003 187 P 0.1785 0.0573 0.7642 188 P 0.1084 0.2104 0.6812 189 H 0.1591 0.1307 0.7102