# This file is the result of combining several RDB files, specifically # T0425.t2k.str2.rdb (weight 1.54425) # T0425.t2k.str4.rdb (weight 0.924988) # T0425.t2k.pb.rdb (weight 0.789901) # T0425.t2k.bys.rdb (weight 0.748322) # T0425.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 T0425.t2k.str2.rdb # ============================================ # TARGET T0425 # 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 T0425.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 100.403 # # ============================================ # Comments from T0425.t2k.str4.rdb # ============================================ # TARGET T0425 # 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 T0425.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 100.403 # # ============================================ # Comments from T0425.t2k.pb.rdb # ============================================ # TARGET T0425 # 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 T0425.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 100.403 # # ============================================ # Comments from T0425.t2k.bys.rdb # ============================================ # TARGET T0425 # 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 T0425.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 100.403 # # ============================================ # Comments from T0425.t2k.alpha.rdb # ============================================ # TARGET T0425 # 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 T0425.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 100.403 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.2948 0.0655 0.6398 2 S 0.2825 0.0486 0.6689 3 K 0.5149 0.0178 0.4672 4 I 0.7628 0.0070 0.2302 5 I 0.8142 0.0049 0.1809 6 C 0.8023 0.0053 0.1924 7 L 0.7776 0.0111 0.2113 8 T 0.6560 0.0103 0.3337 9 A 0.2879 0.1723 0.5398 10 G 0.1643 0.1310 0.7047 11 H 0.1429 0.1843 0.6727 12 S 0.1282 0.1580 0.7138 13 N 0.1508 0.1621 0.6871 14 T 0.1756 0.1427 0.6818 15 D 0.1878 0.1119 0.7003 16 P 0.0792 0.3369 0.5839 17 G 0.1011 0.2378 0.6611 18 A 0.1912 0.2646 0.5442 19 V 0.2192 0.2060 0.5748 20 N 0.1504 0.1396 0.7100 21 G 0.0902 0.1484 0.7614 22 S 0.1505 0.1683 0.6813 23 D 0.1985 0.2759 0.5255 24 R 0.1658 0.4433 0.3908 25 E 0.1095 0.6606 0.2299 26 A 0.0436 0.8095 0.1468 27 D 0.0262 0.8505 0.1233 28 L 0.0133 0.8928 0.0939 29 A 0.0087 0.9154 0.0759 30 Q 0.0084 0.9169 0.0747 31 D 0.0083 0.9239 0.0678 32 M 0.0083 0.9220 0.0697 33 R 0.0083 0.9237 0.0680 34 N 0.0083 0.9246 0.0672 35 I 0.0083 0.9246 0.0672 36 V 0.0083 0.9220 0.0697 37 A 0.0083 0.9221 0.0696 38 S 0.0083 0.9244 0.0673 39 I 0.0084 0.9183 0.0733 40 L 0.0086 0.9062 0.0852 41 R 0.0096 0.8366 0.1538 42 N 0.0192 0.6336 0.3472 43 D 0.0552 0.2884 0.6564 44 Y 0.0739 0.1164 0.8097 45 G 0.1666 0.0738 0.7596 46 L 0.4774 0.0271 0.4955 47 T 0.7205 0.0118 0.2677 48 V 0.7774 0.0078 0.2149 49 K 0.7690 0.0089 0.2221 50 T 0.6944 0.0142 0.2914 51 D 0.4545 0.0408 0.5047 52 G 0.2817 0.0870 0.6312 53 T 0.1665 0.1378 0.6957 54 G 0.1436 0.1230 0.7334 55 K 0.2296 0.1292 0.6412 56 G 0.2566 0.0974 0.6461 57 N 0.2903 0.0833 0.6264 58 M 0.2711 0.0643 0.6646 59 P 0.1928 0.1819 0.6253 60 L 0.0776 0.6452 0.2773 61 R 0.0334 0.8246 0.1420 62 D 0.0207 0.8808 0.0985 63 A 0.0135 0.9035 0.0830 64 V 0.0139 0.9052 0.0809 65 K 0.0129 0.9000 0.0871 66 L 0.0154 0.8321 0.1525 67 I 0.0319 0.7363 0.2318 68 R 0.0662 0.2469 0.6870 69 G 0.0511 0.0651 0.8838 70 S 0.2085 0.0405 0.7510 71 D 0.3779 0.0360 0.5861 72 V 0.7195 0.0155 0.2650 73 A 0.7705 0.0082 0.2213 74 I 0.8027 0.0076 0.1897 75 E 0.7907 0.0090 0.2002 76 F 0.7575 0.0236 0.2190 77 H 0.6798 0.0449 0.2753 78 T 0.4374 0.1508 0.4119 79 N 0.2747 0.2036 0.5217 80 A 0.1628 0.3111 0.5261 81 A 0.1593 0.2534 0.5874 82 A 0.1381 0.2128 0.6491 83 N 0.1616 0.1343 0.7041 84 K 0.1156 0.2809 0.6035 85 T 0.2118 0.1958 0.5924 86 A 0.3025 0.1344 0.5632 87 T 0.3234 0.0944 0.5821 88 G 0.4918 0.0520 0.4562 89 I 0.6910 0.0227 0.2863 90 E 0.7631 0.0142 0.2227 91 A 0.7871 0.0111 0.2018 92 L 0.7622 0.0162 0.2215 93 S 0.6882 0.0193 0.2925 94 T 0.4113 0.0215 0.5672 95 P 0.1744 0.1791 0.6465 96 K 0.0931 0.2729 0.6340 97 N 0.0934 0.2682 0.6384 98 K 0.0743 0.4606 0.4651 99 R 0.0674 0.6263 0.3063 100 W 0.0474 0.7785 0.1741 101 C 0.0225 0.8653 0.1121 102 Q 0.0134 0.8971 0.0895 103 V 0.0123 0.8974 0.0903 104 L 0.0106 0.8985 0.0910 105 G 0.0094 0.8955 0.0951 106 K 0.0107 0.8911 0.0982 107 A 0.0130 0.8858 0.1012 108 V 0.0151 0.8667 0.1182 109 A 0.0192 0.8456 0.1351 110 K 0.0272 0.8187 0.1541 111 K 0.0509 0.7176 0.2315 112 T 0.0611 0.5543 0.3846 113 G 0.0853 0.4147 0.5001 114 W 0.1877 0.4425 0.3697 115 K 0.2465 0.4003 0.3532 116 L 0.2630 0.3155 0.4216 117 R 0.2124 0.2140 0.5736 118 G 0.1506 0.1535 0.6959 119 E 0.1621 0.2123 0.6256 120 D 0.1459 0.1700 0.6840 121 G 0.1236 0.1776 0.6987 122 F 0.2004 0.1248 0.6748 123 K 0.2426 0.0770 0.6804 124 P 0.2169 0.1421 0.6410 125 D 0.2112 0.1968 0.5921 126 N 0.2131 0.2227 0.5642 127 A 0.2332 0.1666 0.6002 128 G 0.2362 0.1418 0.6220 129 Q 0.2845 0.1240 0.5914 130 H 0.5372 0.0633 0.3994 131 S 0.7117 0.0283 0.2600 132 R 0.7722 0.0226 0.2052 133 L 0.7325 0.0392 0.2283 134 A 0.6359 0.0741 0.2900 135 Y 0.4570 0.1196 0.4233 136 A 0.2402 0.2115 0.5483 137 Q 0.2003 0.1565 0.6432 138 A 0.2384 0.1069 0.6547 139 G 0.2645 0.1243 0.6112 140 G 0.4530 0.0763 0.4707 141 I 0.7108 0.0343 0.2549 142 V 0.7601 0.0240 0.2159 143 F 0.7355 0.0263 0.2382 144 E 0.6234 0.0224 0.3542 145 P 0.5177 0.0790 0.4033 146 F 0.5052 0.0943 0.4005 147 F 0.5448 0.0883 0.3669 148 I 0.4988 0.0944 0.4068 149 S 0.3280 0.1015 0.5705 150 N 0.2079 0.0311 0.7610 151 D 0.0305 0.6495 0.3200 152 T 0.0204 0.7775 0.2020 153 D 0.0179 0.8558 0.1263 154 L 0.0132 0.8916 0.0952 155 A 0.0120 0.8903 0.0977 156 L 0.0172 0.8080 0.1748 157 F 0.0320 0.7191 0.2489 158 K 0.0721 0.4501 0.4779 159 T 0.1258 0.2741 0.6001 160 T 0.0233 0.6430 0.3337 161 K 0.0225 0.7363 0.2412 162 W 0.0269 0.7526 0.2205 163 G 0.0229 0.8160 0.1610 164 I 0.0249 0.8680 0.1071 165 C 0.0183 0.8900 0.0917 166 R 0.0180 0.8972 0.0848 167 A 0.0149 0.9050 0.0801 168 I 0.0135 0.9077 0.0789 169 A 0.0152 0.9051 0.0798 170 D 0.0094 0.9162 0.0744 171 A 0.0087 0.9150 0.0763 172 I 0.0084 0.9155 0.0761 173 A 0.0085 0.9177 0.0738 174 M 0.0085 0.9176 0.0739 175 E 0.0088 0.9014 0.0899 176 L 0.0099 0.8569 0.1333 177 G 0.0204 0.7659 0.2136 178 A 0.0403 0.6870 0.2727 179 A 0.0477 0.6196 0.3326 180 K 0.1046 0.4053 0.4901 181 V 0.1884 0.2345 0.5772