# This file is the result of combining several RDB files, specifically # 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) # 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.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 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 S 0.1919 0.2170 0.5911 2 N 0.1754 0.2500 0.5747 3 A 0.1881 0.2762 0.5357 4 M 0.2192 0.2450 0.5358 5 R 0.2310 0.1937 0.5753 6 K 0.2052 0.2199 0.5749 7 D 0.1730 0.2482 0.5788 8 E 0.1397 0.3402 0.5201 9 T 0.1538 0.2829 0.5633 10 S 0.1542 0.2741 0.5717 11 N 0.1715 0.1898 0.6387 12 T 0.2159 0.1218 0.6623 13 S 0.2341 0.0467 0.7192 14 P 0.1767 0.2005 0.6228 15 D 0.1914 0.2499 0.5587 16 I 0.2885 0.2600 0.4515 17 S 0.3672 0.2019 0.4309 18 V 0.4317 0.1614 0.4069 19 A 0.4057 0.0869 0.5074 20 Q 0.2836 0.0375 0.6789 21 P 0.2000 0.1360 0.6640 22 A 0.1312 0.2562 0.6126 23 S 0.1284 0.2444 0.6273 24 A 0.2236 0.1248 0.6516 25 L 0.3798 0.0693 0.5509 26 R 0.5625 0.0352 0.4023 27 Y 0.7090 0.0134 0.2776 28 H 0.7379 0.0116 0.2505 29 L 0.7000 0.0109 0.2891 30 R 0.5676 0.0172 0.4152 31 P 0.3619 0.0165 0.6216 32 P 0.2597 0.0729 0.6674 33 R 0.1871 0.0407 0.7722 34 R 0.0772 0.4465 0.4764 35 N 0.0575 0.4756 0.4669 36 D 0.1023 0.4561 0.4416 37 G 0.0142 0.7622 0.2236 38 A 0.0102 0.8740 0.1158 39 A 0.0093 0.9161 0.0746 40 I 0.0086 0.9211 0.0703 41 H 0.0085 0.9207 0.0708 42 Q 0.0087 0.9187 0.0727 43 L 0.0092 0.9098 0.0810 44 V 0.0121 0.8636 0.1243 45 S 0.0148 0.7452 0.2400 46 E 0.0399 0.4481 0.5120 47 C 0.1428 0.1176 0.7395 48 P 0.1478 0.0787 0.7735 49 P 0.1402 0.1834 0.6764 50 L 0.1485 0.2042 0.6473 51 D 0.1648 0.1685 0.6667 52 L 0.0680 0.4927 0.4393 53 N 0.0643 0.5124 0.4232 54 S 0.0505 0.6883 0.2612 55 L 0.0213 0.8258 0.1529 56 Y 0.0180 0.8757 0.1063 57 A 0.0183 0.8965 0.0852 58 Y 0.0192 0.8938 0.0870 59 L 0.0186 0.8955 0.0859 60 L 0.0223 0.8745 0.1032 61 L 0.0401 0.7826 0.1773 62 C 0.0700 0.6332 0.2968 63 E 0.0776 0.4619 0.4605 64 H 0.1214 0.2469 0.6317 65 H 0.1644 0.1721 0.6636 66 A 0.2015 0.1473 0.6512 67 H 0.3817 0.0686 0.5497 68 T 0.6743 0.0210 0.3047 69 C 0.7884 0.0071 0.2046 70 V 0.8213 0.0046 0.1741 71 V 0.8208 0.0054 0.1738 72 A 0.8020 0.0064 0.1916 73 E 0.7665 0.0152 0.2183 74 S 0.4776 0.0122 0.5102 75 P 0.1346 0.2213 0.6441 76 G 0.0675 0.1428 0.7897 77 G 0.1121 0.0710 0.8170 78 R 0.4429 0.0217 0.5354 79 I 0.6492 0.0126 0.3382 80 D 0.6122 0.0417 0.3462 81 G 0.7529 0.0169 0.2302 82 F 0.7620 0.0172 0.2208 83 V 0.8052 0.0107 0.1841 84 S 0.7900 0.0139 0.1961 85 A 0.7498 0.0279 0.2223 86 Y 0.6831 0.0345 0.2824 87 L 0.5399 0.0516 0.4085 88 L 0.3311 0.0424 0.6265 89 P 0.1676 0.1746 0.6578 90 T 0.1416 0.1333 0.7251 91 R 0.1820 0.0763 0.7417 92 P 0.1407 0.2267 0.6326 93 D 0.1863 0.2651 0.5486 94 V 0.4812 0.1629 0.3559 95 L 0.6361 0.0997 0.2642 96 F 0.7472 0.0485 0.2043 97 V 0.7385 0.0494 0.2122 98 W 0.6815 0.0876 0.2310 99 Q 0.7392 0.0441 0.2167 100 V 0.7322 0.0574 0.2103 101 A 0.7123 0.0427 0.2449 102 V 0.6398 0.0588 0.3013 103 H 0.3499 0.0471 0.6030 104 S 0.0474 0.5500 0.4027 105 R 0.0234 0.6273 0.3493 106 A 0.0558 0.5675 0.3767 107 R 0.0763 0.3967 0.5269 108 G 0.0621 0.3236 0.6143 109 H 0.0670 0.4688 0.4641 110 R 0.0531 0.5633 0.3836 111 L 0.0325 0.7501 0.2175 112 G 0.0129 0.8752 0.1119 113 R 0.0085 0.9129 0.0786 114 A 0.0083 0.9204 0.0713 115 M 0.0083 0.9190 0.0726 116 L 0.0084 0.9171 0.0745 117 G 0.0083 0.9210 0.0707 118 H 0.0083 0.9195 0.0722 119 I 0.0084 0.9200 0.0717 120 L 0.0083 0.9202 0.0715 121 E 0.0083 0.9177 0.0740 122 R 0.0085 0.9084 0.0830 123 Q 0.0097 0.8895 0.1008 124 E 0.0095 0.8539 0.1366 125 C 0.0152 0.7637 0.2211 126 R 0.0555 0.3001 0.6445 127 H 0.0531 0.0985 0.8485 128 V 0.2192 0.0719 0.7089 129 R 0.3415 0.1006 0.5579 130 H 0.7203 0.0283 0.2514 131 L 0.7358 0.0162 0.2480 132 E 0.7713 0.0214 0.2072 133 T 0.7913 0.0156 0.1931 134 T 0.7586 0.0148 0.2266 135 V 0.6547 0.0244 0.3209 136 G 0.2525 0.0288 0.7187 137 P 0.0828 0.3007 0.6165 138 D 0.0534 0.2998 0.6468 139 N 0.0576 0.4131 0.5294 140 Q 0.0187 0.7757 0.2056 141 A 0.0107 0.8888 0.1005 142 S 0.0086 0.9179 0.0735 143 R 0.0084 0.9204 0.0713 144 R 0.0083 0.9201 0.0715 145 T 0.0084 0.9185 0.0731 146 F 0.0088 0.9085 0.0827 147 A 0.0089 0.8987 0.0925 148 G 0.0107 0.8165 0.1727 149 L 0.0213 0.6963 0.2823 150 A 0.0467 0.4836 0.4697 151 G 0.0418 0.4125 0.5457 152 E 0.0614 0.3894 0.5491 153 R 0.1103 0.1769 0.7128 154 G 0.1655 0.0851 0.7494 155 A 0.4809 0.0315 0.4875 156 H 0.6182 0.0273 0.3545 157 V 0.6293 0.0363 0.3344 158 S 0.4910 0.0684 0.4405 159 E 0.3723 0.0628 0.5649 160 Q 0.3769 0.0395 0.5836 161 P 0.3681 0.0810 0.5509 162 F 0.3613 0.1389 0.4999 163 F 0.3277 0.2066 0.4657 164 D 0.3347 0.2296 0.4357 165 R 0.4011 0.2197 0.3792 166 Q 0.4521 0.1635 0.3844 167 A 0.3643 0.1851 0.4506 168 F 0.2030 0.1806 0.6164 169 G 0.1022 0.1132 0.7846 170 G 0.0941 0.0963 0.8096 171 A 0.1904 0.1249 0.6847 172 D 0.2120 0.1913 0.5967 173 H 0.1708 0.3673 0.4619 174 D 0.1499 0.4361 0.4140 175 D 0.0349 0.7863 0.1788 176 E 0.0485 0.8352 0.1163 177 M 0.0438 0.8627 0.0935 178 L 0.0714 0.8092 0.1194 179 L 0.1332 0.7128 0.1540 180 R 0.2236 0.5165 0.2599 181 I 0.2406 0.2883 0.4711 182 G 0.2058 0.0857 0.7085 183 P 0.1402 0.2008 0.6590 184 F 0.1518 0.2215 0.6267 185 T 0.1707 0.1399 0.6894 186 H 0.2248 0.0533 0.7219 187 P 0.1927 0.0418 0.7655 188 P 0.1572 0.1532 0.6896 189 H 0.1312 0.1602 0.7086