# This file is the result of combining several RDB files, specifically # T0322.t2k.dssp-ebghstl.rdb (weight 1.53986) # T0322.t2k.stride-ebghtl.rdb (weight 1.24869) # T0322.t2k.str2.rdb (weight 1.54758) # T0322.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 T0322.t2k.dssp-ebghstl.rdb # ============================================ # TARGET T0322 # 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 T0322.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 307 # # ============================================ # Comments from T0322.t2k.stride-ebghtl.rdb # ============================================ # TARGET T0322 # 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 T0322.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 307 # # ============================================ # Comments from T0322.t2k.str2.rdb # ============================================ # TARGET T0322 # 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 T0322.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 307 # # ============================================ # Comments from T0322.t2k.alpha.rdb # ============================================ # TARGET T0322 # 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 T0322.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 307 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.1020 0.0620 0.8360 2 S 0.1458 0.0830 0.7712 3 D 0.0843 0.1386 0.7771 4 D 0.0883 0.1420 0.7697 5 L 0.0675 0.2575 0.6751 6 T 0.0717 0.2303 0.6980 7 D 0.0729 0.1911 0.7360 8 A 0.0688 0.1497 0.7815 9 Q 0.0623 0.1716 0.7662 10 T 0.0163 0.7610 0.2227 11 A 0.0097 0.8488 0.1416 12 A 0.0105 0.8557 0.1339 13 I 0.0136 0.8600 0.1264 14 P 0.0091 0.8546 0.1363 15 E 0.0067 0.8962 0.0971 16 G 0.0079 0.8817 0.1104 17 F 0.0105 0.8792 0.1103 18 S 0.0116 0.8371 0.1513 19 Q 0.0143 0.7619 0.2238 20 L 0.0256 0.6139 0.3605 21 N 0.0469 0.3725 0.5805 22 W 0.0598 0.3146 0.6256 23 S 0.0457 0.2975 0.6568 24 R 0.0431 0.2504 0.7065 25 G 0.0479 0.2874 0.6647 26 F 0.0257 0.5620 0.4124 27 G 0.0357 0.6799 0.2844 28 R 0.0449 0.6706 0.2845 29 Q 0.0888 0.5683 0.3429 30 I 0.1332 0.4113 0.4555 31 G 0.1474 0.1774 0.6752 32 P 0.1407 0.0738 0.7855 33 L 0.4580 0.0446 0.4974 34 F 0.7655 0.0194 0.2151 35 E 0.8598 0.0123 0.1279 36 H 0.8119 0.0236 0.1645 37 R 0.8164 0.0143 0.1694 38 E 0.6675 0.0261 0.3064 39 G 0.3196 0.0267 0.6537 40 P 0.0705 0.0490 0.8805 41 G 0.1340 0.0349 0.8311 42 Q 0.6935 0.0085 0.2979 43 A 0.8991 0.0035 0.0974 44 R 0.9240 0.0036 0.0724 45 L 0.9197 0.0038 0.0765 46 A 0.9096 0.0043 0.0861 47 F 0.8670 0.0053 0.1277 48 R 0.8172 0.0050 0.1778 49 V 0.6077 0.0137 0.3786 50 E 0.2685 0.0181 0.7134 51 E 0.0962 0.3149 0.5889 52 H 0.0576 0.3568 0.5857 53 H 0.0854 0.3465 0.5681 54 T 0.1679 0.1777 0.6544 55 N 0.1052 0.1022 0.7926 56 G 0.0530 0.1959 0.7512 57 L 0.0746 0.1882 0.7372 58 G 0.0853 0.2272 0.6875 59 N 0.1949 0.4339 0.3712 60 C 0.2503 0.5541 0.1956 61 H 0.1163 0.6620 0.2217 62 G 0.0250 0.7895 0.1854 63 G 0.0147 0.8603 0.1251 64 M 0.0071 0.9375 0.0553 65 L 0.0065 0.9475 0.0460 66 M 0.0058 0.9496 0.0446 67 S 0.0056 0.9359 0.0586 68 F 0.0048 0.9510 0.0442 69 A 0.0049 0.9461 0.0489 70 D 0.0053 0.9444 0.0503 71 M 0.0051 0.9523 0.0426 72 A 0.0049 0.9524 0.0427 73 W 0.0048 0.9554 0.0398 74 G 0.0048 0.9529 0.0422 75 R 0.0058 0.9488 0.0454 76 I 0.0075 0.9432 0.0493 77 I 0.0102 0.9169 0.0729 78 S 0.0243 0.8353 0.1404 79 L 0.0381 0.6662 0.2956 80 Q 0.0538 0.3169 0.6293 81 K 0.0515 0.1488 0.7997 82 S 0.0468 0.0713 0.8819 83 Y 0.1563 0.0314 0.8123 84 S 0.4068 0.0221 0.5711 85 W 0.8028 0.0076 0.1896 86 V 0.8974 0.0044 0.0982 87 T 0.9157 0.0032 0.0811 88 V 0.8984 0.0054 0.0962 89 R 0.8954 0.0038 0.1007 90 L 0.8351 0.0070 0.1579 91 M 0.8218 0.0060 0.1722 92 C 0.8566 0.0052 0.1382 93 D 0.8684 0.0105 0.1211 94 F 0.8703 0.0093 0.1205 95 L 0.8060 0.0195 0.1745 96 S 0.6793 0.0176 0.3031 97 G 0.5989 0.0209 0.3802 98 A 0.4331 0.0170 0.5499 99 K 0.3372 0.0248 0.6380 100 L 0.0865 0.0866 0.8269 101 G 0.0451 0.0542 0.9007 102 D 0.3359 0.0234 0.6408 103 W 0.8352 0.0040 0.1608 104 V 0.9095 0.0049 0.0856 105 E 0.9229 0.0044 0.0727 106 G 0.9181 0.0045 0.0774 107 E 0.9110 0.0054 0.0836 108 G 0.9018 0.0050 0.0932 109 E 0.9055 0.0049 0.0896 110 L 0.9200 0.0030 0.0770 111 I 0.8599 0.0137 0.1263 112 S 0.7753 0.0125 0.2122 113 E 0.3037 0.0541 0.6421 114 E 0.1298 0.0346 0.8356 115 D 0.3039 0.0346 0.6614 116 M 0.7171 0.0089 0.2741 117 L 0.8901 0.0040 0.1059 118 F 0.9124 0.0040 0.0836 119 T 0.9288 0.0030 0.0682 120 V 0.9208 0.0039 0.0753 121 R 0.9293 0.0030 0.0677 122 G 0.9228 0.0039 0.0733 123 R 0.9289 0.0034 0.0677 124 I 0.9262 0.0032 0.0706 125 W 0.8830 0.0090 0.1080 126 A 0.6222 0.0182 0.3596 127 G 0.0582 0.0858 0.8560 128 E 0.0542 0.0383 0.9075 129 R 0.1744 0.0833 0.7423 130 T 0.7061 0.0446 0.2494 131 L 0.8972 0.0210 0.0818 132 I 0.8777 0.0414 0.0808 133 T 0.7955 0.1049 0.0996 134 G 0.6818 0.1470 0.1712 135 T 0.5143 0.1458 0.3399 136 G 0.4904 0.0698 0.4398 137 V 0.6273 0.0769 0.2958 138 F 0.7402 0.0971 0.1627 139 K 0.7575 0.1079 0.1346 140 A 0.7013 0.1316 0.1671 141 L 0.5849 0.1308 0.2842 142 S 0.3891 0.1093 0.5016 143 A 0.1311 0.1018 0.7671 144 R 0.0962 0.0512 0.8526 145 K 0.1215 0.0245 0.8540 146 P 0.0929 0.0280 0.8792 147 R 0.0575 0.0434 0.8990 148 P 0.0393 0.2425 0.7181 149 G 0.0312 0.2589 0.7100 150 E 0.0576 0.4312 0.5113 151 L 0.0517 0.6916 0.2568 152 A 0.0393 0.7447 0.2160 153 Y 0.0361 0.7870 0.1769 154 K 0.0408 0.7758 0.1834 155 E 0.0443 0.7190 0.2367 156 E 0.0409 0.6176 0.3415 157 A 0.0350 0.3087 0.6563