# This file is the result of combining several RDB files, specifically # T0301.t2k.dssp-ebghstl.rdb (weight 1.53986) # T0301.t2k.stride-ebghtl.rdb (weight 1.24869) # T0301.t2k.str2.rdb (weight 1.54758) # T0301.t2k.alpha.rdb (weight 0.659012) # 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 T0301.t2k.dssp-ebghstl.rdb # ============================================ # TARGET T0301 # Using neural net t2k-5740-IDaaHr-5-15-7-15-9-15-13-ebghstl-seeded.net # This is a 4-layer network, with # window units # 5 15 # 7 15 # 9 15 # 13 7 (1 EBGHSTL ) # The input amino acid frequencies were determined from # alignment T0301.t2k-thin90.a2m.gz # with weighted counts, using HenikoffWeight(-1 bits/column, 1) # Counts were regularized to probabilities using # /projects/compbio/lib/recode3.20comp # Total sequence weight for alignment was 115 # # ============================================ # Comments from T0301.t2k.stride-ebghtl.rdb # ============================================ # TARGET T0301 # Using neural net t2k-5651-IDaaHr-5-15-7-15-9-15-13-ebghtl-seeded.net # This is a 4-layer network, with # window units # 5 15 # 7 15 # 9 15 # 13 6 (1 EBGHTL ) # The input amino acid frequencies were determined from # alignment T0301.t2k-thin90.a2m.gz # with weighted counts, using HenikoffWeight(-1 bits/column, 1) # Counts were regularized to probabilities using # /projects/compbio/lib/recode3.20comp # Total sequence weight for alignment was 115 # # ============================================ # Comments from T0301.t2k.str2.rdb # ============================================ # TARGET T0301 # Using neural net dunbrack-30pc-1763-t2k-thin90-IDGaaH13-3-13-7-13-9-13-11-t1c2-str2-from-empty.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 T0301.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 10.8792 # # ============================================ # Comments from T0301.t2k.alpha.rdb # ============================================ # TARGET T0301 # Using neural net t2k-5651-IDaaHr-5-15-7-15-9-15-13-alpha-seeded.net # This is a 4-layer network, with # window units # 5 15 # 7 15 # 9 15 # 13 11 (1 ABCDEFGHIST ) # The input amino acid frequencies were determined from # alignment T0301.t2k-thin90.a2m.gz # with weighted counts, using HenikoffWeight(-1 bits/column, 1) # Counts were regularized to probabilities using # /projects/compbio/lib/recode3.20comp # Total sequence weight for alignment was 115 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.0840 0.0428 0.8733 2 A 0.1107 0.0514 0.8379 3 H 0.0967 0.0370 0.8663 4 P 0.0778 0.0693 0.8529 5 P 0.1009 0.1021 0.7970 6 Q 0.1903 0.1684 0.6413 7 I 0.2759 0.0952 0.6290 8 R 0.3189 0.0685 0.6126 9 I 0.3237 0.0296 0.6467 10 P 0.3134 0.0442 0.6424 11 A 0.6523 0.0650 0.2827 12 T 0.7835 0.0661 0.1503 13 Y 0.7848 0.0735 0.1417 14 L 0.6786 0.0592 0.2622 15 R 0.4025 0.0538 0.5437 16 G 0.1536 0.0679 0.7784 17 G 0.0988 0.0850 0.8162 18 T 0.1293 0.0791 0.7916 19 S 0.1378 0.1431 0.7191 20 K 0.1419 0.1663 0.6918 21 G 0.2308 0.1365 0.6328 22 V 0.4688 0.1473 0.3839 23 F 0.6381 0.1040 0.2579 24 F 0.6679 0.0749 0.2572 25 R 0.4968 0.0648 0.4384 26 L 0.0706 0.5189 0.4105 27 E 0.0207 0.4962 0.4830 28 D 0.0333 0.4458 0.5209 29 L 0.0697 0.0842 0.8460 30 P 0.0513 0.1294 0.8193 31 E 0.0362 0.3167 0.6471 32 S 0.0404 0.3742 0.5854 33 C 0.0343 0.5047 0.4610 34 R 0.0529 0.4251 0.5220 35 V 0.0547 0.3655 0.5798 36 P 0.0269 0.4786 0.4945 37 G 0.0182 0.6564 0.3253 38 E 0.0078 0.8476 0.1446 39 A 0.0098 0.8743 0.1159 40 R 0.0067 0.9018 0.0915 41 D 0.0055 0.9220 0.0724 42 R 0.0060 0.8960 0.0979 43 L 0.0096 0.8658 0.1246 44 F 0.0203 0.8008 0.1789 45 M 0.0116 0.8341 0.1543 46 R 0.0211 0.7645 0.2144 47 V 0.0439 0.6669 0.2892 48 I 0.0803 0.3055 0.6143 49 G 0.0683 0.0819 0.8498 50 S 0.0731 0.0496 0.8773 51 P 0.0661 0.0847 0.8492 52 D 0.0951 0.0945 0.8103 53 P 0.0643 0.1889 0.7467 54 Y 0.0781 0.1566 0.7653 55 A 0.0783 0.2342 0.6875 56 A 0.1653 0.1587 0.6760 57 H 0.3256 0.1220 0.5524 58 I 0.3936 0.1091 0.4974 59 D 0.2385 0.0948 0.6667 60 G 0.1580 0.0824 0.7596 61 M 0.1749 0.0707 0.7544 62 G 0.1359 0.0561 0.8080 63 G 0.1297 0.0602 0.8101 64 A 0.1977 0.0640 0.7384 65 T 0.1401 0.0757 0.7842 66 S 0.1084 0.1319 0.7597 67 S 0.1236 0.1212 0.7552 68 T 0.2405 0.0768 0.6826 69 S 0.2326 0.0298 0.7375 70 K 0.4926 0.0203 0.4871 71 C 0.8632 0.0058 0.1309 72 V 0.9061 0.0043 0.0896 73 I 0.9211 0.0033 0.0756 74 L 0.8524 0.0150 0.1326 75 S 0.5835 0.0117 0.4048 76 K 0.2583 0.0472 0.6945 77 S 0.1358 0.0644 0.7998 78 S 0.0892 0.1116 0.7992 79 Q 0.0730 0.0496 0.8774 80 P 0.0283 0.1144 0.8573 81 G 0.0543 0.0598 0.8860 82 H 0.1662 0.0241 0.8097 83 D 0.3772 0.0167 0.6061 84 V 0.6971 0.0261 0.2769 85 D 0.7837 0.0350 0.1813 86 Y 0.8745 0.0129 0.1126 87 L 0.8885 0.0130 0.0985 88 Y 0.8628 0.0178 0.1194 89 G 0.8275 0.0193 0.1532 90 Q 0.8312 0.0198 0.1490 91 V 0.8430 0.0120 0.1450 92 S 0.7734 0.0113 0.2153 93 I 0.4923 0.0750 0.4327 94 D 0.2102 0.0549 0.7350 95 K 0.1449 0.0852 0.7699 96 P 0.1931 0.1391 0.6678 97 F 0.4494 0.1107 0.4399 98 V 0.6027 0.0477 0.3496 99 D 0.3667 0.0473 0.5860 100 W 0.1250 0.1394 0.7356 101 S 0.0787 0.1282 0.7931 102 G 0.0537 0.1345 0.8118 103 N 0.0610 0.1545 0.7845 104 C 0.0966 0.1573 0.7461 105 G 0.0840 0.2509 0.6651 106 N 0.1107 0.4240 0.4653 107 L 0.0842 0.6320 0.2838 108 S 0.0842 0.6653 0.2505 109 T 0.0862 0.6686 0.2452 110 G 0.0811 0.6838 0.2351 111 A 0.0988 0.6689 0.2322 112 G 0.0477 0.6645 0.2879 113 A 0.0242 0.8316 0.1442 114 F 0.0551 0.8238 0.1211 115 A 0.0923 0.7826 0.1251 116 L 0.1255 0.7160 0.1585 117 H 0.0917 0.6339 0.2744 118 A 0.0823 0.3219 0.5957 119 G 0.0888 0.0781 0.8331 120 L 0.1964 0.0532 0.7504 121 V 0.3625 0.0380 0.5995 122 D 0.1994 0.0529 0.7477 123 P 0.1009 0.3930 0.5061 124 A 0.1053 0.3535 0.5412 125 R 0.1765 0.2956 0.5279 126 I 0.2140 0.0660 0.7200 127 P 0.0978 0.0854 0.8167 128 E 0.0581 0.1086 0.8333 129 D 0.0698 0.0734 0.8568 130 G 0.1554 0.0457 0.7990 131 I 0.5108 0.0120 0.4772 132 C 0.8354 0.0055 0.1591 133 E 0.9177 0.0036 0.0787 134 V 0.9242 0.0034 0.0724 135 R 0.9239 0.0035 0.0726 136 I 0.9239 0.0030 0.0731 137 W 0.8831 0.0116 0.1053 138 Q 0.8419 0.0096 0.1485 139 A 0.5686 0.0418 0.3896 140 N 0.2959 0.0513 0.6528 141 I 0.1250 0.0497 0.8253 142 G 0.1320 0.0446 0.8234 143 K 0.5427 0.0130 0.4443 144 T 0.8534 0.0037 0.1429 145 I 0.9078 0.0049 0.0873 146 I 0.9230 0.0036 0.0734 147 A 0.9088 0.0055 0.0857 148 H 0.8988 0.0046 0.0966 149 V 0.8613 0.0049 0.1338 150 P 0.8354 0.0050 0.1596 151 V 0.4964 0.0149 0.4887 152 S 0.1481 0.0959 0.7560 153 G 0.0629 0.0215 0.9156 154 G 0.1547 0.0325 0.8128 155 Q 0.5652 0.0094 0.4254 156 V 0.8490 0.0050 0.1459 157 Q 0.8055 0.0095 0.1850 158 E 0.7917 0.0192 0.1891 159 T 0.4713 0.0455 0.4832 160 G 0.3135 0.0320 0.6545 161 D 0.3826 0.0361 0.5813 162 F 0.7238 0.0164 0.2598 163 E 0.7701 0.0173 0.2126 164 L 0.7109 0.0217 0.2674 165 D 0.2919 0.0504 0.6578 166 G 0.1405 0.0477 0.8118 167 V 0.2979 0.0375 0.6646 168 T 0.2634 0.0571 0.6795 169 F 0.1656 0.0635 0.7709 170 P 0.1497 0.0839 0.7663 171 A 0.1410 0.1247 0.7343 172 A 0.2442 0.0564 0.6995 173 E 0.4701 0.0276 0.5023 174 I 0.7114 0.0128 0.2758 175 V 0.8432 0.0121 0.1447 176 L 0.8509 0.0103 0.1387 177 E 0.8122 0.0145 0.1733 178 F 0.7017 0.0201 0.2782 179 L 0.4726 0.0363 0.4911 180 D 0.2592 0.0427 0.6981 181 P 0.1137 0.1060 0.7803 182 S 0.0904 0.0795 0.8301 183 D 0.0420 0.0390 0.9189