# This file is the result of combining several RDB files, specifically # T0324.t06.dssp-ebghstl.rdb (weight 1.53986) # T0324.t06.stride-ebghtl.rdb (weight 1.24869) # T0324.t06.str2.rdb (weight 1.54758) # T0324.t06.alpha.rdb (weight 0.659012) # T0324.t04.dssp-ebghstl.rdb (weight 1.53986) # T0324.t04.stride-ebghtl.rdb (weight 1.24869) # T0324.t04.str2.rdb (weight 1.54758) # T0324.t04.alpha.rdb (weight 0.659012) # T0324.t2k.dssp-ebghstl.rdb (weight 1.53986) # T0324.t2k.stride-ebghtl.rdb (weight 1.24869) # T0324.t2k.str2.rdb (weight 1.54758) # T0324.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 T0324.t06.dssp-ebghstl.rdb # ============================================ # TARGET T0324 # Using neural net t06-IDGaaH13-3-13-7-13-9-13-11-ebghstl-dssp-seeded.net # This is a 4-layer network, with # window units # 3 13 # 7 13 # 9 13 # 11 7 (1 EBGHSTL ) # The input amino acid frequencies were determined from # alignment T0324.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 4841 # # ============================================ # Comments from T0324.t06.stride-ebghtl.rdb # ============================================ # TARGET T0324 # Using neural net t06-IDGaaH13-3-13-7-13-9-13-11-ebghtl-stride-seeded.net # This is a 4-layer network, with # window units # 3 13 # 7 13 # 9 13 # 11 6 (1 EBGHTL ) # The input amino acid frequencies were determined from # alignment T0324.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 4841 # # ============================================ # Comments from T0324.t06.str2.rdb # ============================================ # TARGET T0324 # Using neural net 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 T0324.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 4841 # # ============================================ # Comments from T0324.t06.alpha.rdb # ============================================ # TARGET T0324 # Using neural net 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 T0324.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 4841 # # ============================================ # Comments from T0324.t04.dssp-ebghstl.rdb # ============================================ # TARGET T0324 # Using neural net t06-IDGaaH13-3-13-7-13-9-13-11-ebghstl-dssp-seeded.net # This is a 4-layer network, with # window units # 3 13 # 7 13 # 9 13 # 11 7 (1 EBGHSTL ) # The input amino acid frequencies were determined from # alignment T0324.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 2280 # # ============================================ # Comments from T0324.t04.stride-ebghtl.rdb # ============================================ # TARGET T0324 # Using neural net t04-2621-IDGaaH13-3-13-7-13-9-13-11-ebghtl-stride-seeded.net # This is a 4-layer network, with # window units # 3 13 # 7 13 # 9 13 # 11 6 (1 EBGHTL ) # The input amino acid frequencies were determined from # alignment T0324.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 2280 # # ============================================ # Comments from T0324.t04.str2.rdb # ============================================ # TARGET T0324 # Using neural net 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 T0324.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 2280 # # ============================================ # Comments from T0324.t04.alpha.rdb # ============================================ # TARGET T0324 # Using neural net t04-2621-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 T0324.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 2280 # # ============================================ # Comments from T0324.t2k.dssp-ebghstl.rdb # ============================================ # TARGET T0324 # 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 T0324.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 1750 # # ============================================ # Comments from T0324.t2k.stride-ebghtl.rdb # ============================================ # TARGET T0324 # 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 T0324.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 1750 # # ============================================ # Comments from T0324.t2k.str2.rdb # ============================================ # TARGET T0324 # 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 T0324.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 1750 # # ============================================ # Comments from T0324.t2k.alpha.rdb # ============================================ # TARGET T0324 # 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 T0324.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 1750 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.0880 0.0274 0.8846 2 T 0.2293 0.0155 0.7552 3 Y 0.4785 0.0087 0.5129 4 Q 0.7040 0.0260 0.2701 5 A 0.9108 0.0041 0.0851 6 L 0.9260 0.0033 0.0707 7 M 0.9192 0.0042 0.0766 8 F 0.8695 0.0057 0.1248 9 D 0.4769 0.0112 0.5119 10 I 0.0988 0.1043 0.7969 11 D 0.0745 0.0359 0.8896 12 G 0.1135 0.0576 0.8289 13 T 0.4355 0.0539 0.5106 14 L 0.6555 0.0574 0.2871 15 T 0.5498 0.0853 0.3649 16 N 0.2323 0.0869 0.6807 17 S 0.0610 0.1612 0.7778 18 Q 0.0325 0.7281 0.2394 19 P 0.0070 0.9108 0.0823 20 A 0.0064 0.9255 0.0681 21 Y 0.0054 0.9388 0.0557 22 T 0.0049 0.9473 0.0479 23 T 0.0048 0.9542 0.0410 24 V 0.0047 0.9551 0.0402 25 M 0.0047 0.9560 0.0393 26 R 0.0048 0.9556 0.0396 27 E 0.0048 0.9549 0.0403 28 V 0.0047 0.9552 0.0401 29 L 0.0049 0.9473 0.0478 30 A 0.0054 0.9294 0.0652 31 T 0.0076 0.8691 0.1233 32 Y 0.0437 0.5164 0.4399 33 G 0.0361 0.0410 0.9229 34 K 0.0623 0.0314 0.9063 35 P 0.0937 0.0387 0.8675 36 F 0.0901 0.0923 0.8175 37 S 0.0668 0.1040 0.8291 38 P 0.0301 0.7490 0.2208 39 A 0.0104 0.8909 0.0988 40 Q 0.0108 0.9000 0.0892 41 A 0.0142 0.9008 0.0851 42 Q 0.0163 0.8733 0.1105 43 K 0.0180 0.8152 0.1668 44 T 0.0218 0.7215 0.2566 45 F 0.0394 0.5348 0.4258 46 P 0.0470 0.4168 0.5361 47 M 0.0521 0.3662 0.5817 48 A 0.0498 0.3918 0.5584 49 A 0.0469 0.5304 0.4227 50 E 0.0259 0.7575 0.2167 51 Q 0.0182 0.8523 0.1295 52 A 0.0199 0.8734 0.1067 53 M 0.0205 0.8827 0.0969 54 T 0.0219 0.8767 0.1015 55 E 0.0226 0.8458 0.1316 56 L 0.0222 0.7737 0.2041 57 G 0.0329 0.5770 0.3900 58 I 0.0329 0.3998 0.5674 59 A 0.0364 0.4278 0.5358 60 A 0.0284 0.5035 0.4681 61 S 0.0291 0.4977 0.4732 62 E 0.0224 0.6001 0.3775 63 F 0.0121 0.7211 0.2668 64 D 0.0101 0.8226 0.1673 65 H 0.0089 0.8375 0.1536 66 F 0.0100 0.8785 0.1114 67 Q 0.0067 0.9066 0.0868 68 A 0.0064 0.9141 0.0795 69 Q 0.0064 0.9029 0.0906 70 Y 0.0060 0.9159 0.0781 71 E 0.0057 0.9355 0.0588 72 D 0.0058 0.9341 0.0602 73 V 0.0064 0.9282 0.0654 74 M 0.0070 0.9163 0.0767 75 A 0.0078 0.8867 0.1054 76 S 0.0115 0.7835 0.2050 77 H 0.0223 0.5792 0.3985 78 Y 0.0300 0.4392 0.5307 79 D 0.0282 0.4052 0.5667 80 Q 0.0407 0.2900 0.6693 81 I 0.1227 0.1466 0.7307 82 E 0.1583 0.1174 0.7244 83 L 0.1664 0.1443 0.6894 84 Y 0.0734 0.0991 0.8275 85 P 0.0192 0.3058 0.6750 86 G 0.0349 0.2838 0.6813 87 I 0.0140 0.7950 0.1910 88 T 0.0052 0.9352 0.0597 89 S 0.0083 0.9319 0.0598 90 L 0.0048 0.9490 0.0461 91 F 0.0051 0.9408 0.0541 92 E 0.0052 0.9029 0.0919 93 Q 0.0062 0.7734 0.2205 94 L 0.0176 0.6542 0.3282 95 P 0.0206 0.5809 0.3985 96 S 0.0333 0.2745 0.6921 97 E 0.0376 0.0673 0.8951 98 L 0.2401 0.0137 0.7463 99 R 0.5053 0.0112 0.4835 100 L 0.9142 0.0048 0.0810 101 G 0.9268 0.0037 0.0695 102 I 0.9286 0.0033 0.0680 103 V 0.8765 0.0075 0.1160 104 T 0.4299 0.0275 0.5426 105 S 0.1030 0.0374 0.8596 106 Q 0.0605 0.0998 0.8397 107 R 0.0548 0.2888 0.6565 108 R 0.0134 0.7779 0.2087 109 N 0.0079 0.8868 0.1053 110 E 0.0076 0.9122 0.0802 111 L 0.0051 0.9450 0.0500 112 E 0.0051 0.9518 0.0430 113 S 0.0050 0.9220 0.0730 114 G 0.0053 0.9118 0.0828 115 M 0.0057 0.9040 0.0903 116 R 0.0060 0.8558 0.1382 117 S 0.0091 0.7729 0.2180 118 Y 0.0502 0.3966 0.5533 119 P 0.0549 0.0732 0.8719 120 F 0.0720 0.1734 0.7546 121 M 0.0919 0.3616 0.5465 122 M 0.1362 0.4084 0.4553 123 R 0.2780 0.2726 0.4495 124 M 0.3704 0.0806 0.5489 125 A 0.4895 0.0962 0.4143 126 V 0.8481 0.0326 0.1193 127 T 0.8805 0.0195 0.1000 128 I 0.8637 0.0185 0.1178 129 S 0.5756 0.0348 0.3895 130 A 0.1387 0.2032 0.6581 131 D 0.0576 0.2889 0.6535 132 D 0.0672 0.3240 0.6088 133 T 0.0874 0.2091 0.7035 134 P 0.0664 0.1632 0.7704 135 K 0.0718 0.1344 0.7938 136 R 0.0797 0.0681 0.8522 137 K 0.1009 0.0428 0.8563 138 P 0.0924 0.0535 0.8541 139 D 0.0844 0.0521 0.8635 140 P 0.0262 0.5712 0.4027 141 L 0.0123 0.8178 0.1700 142 P 0.0058 0.9253 0.0690 143 L 0.0049 0.9569 0.0382 144 L 0.0048 0.9584 0.0367 145 T 0.0048 0.9595 0.0357 146 A 0.0047 0.9594 0.0359 147 L 0.0048 0.9579 0.0373 148 E 0.0053 0.9478 0.0469 149 K 0.0067 0.9035 0.0898 150 V 0.0463 0.4200 0.5337 151 N 0.0424 0.0208 0.9368 152 V 0.0769 0.0085 0.9146 153 A 0.0788 0.0113 0.9100 154 P 0.0382 0.5332 0.4286 155 Q 0.0287 0.5793 0.3919 156 N 0.1781 0.4722 0.3497 157 A 0.7695 0.0276 0.2029 158 L 0.8712 0.0102 0.1186 159 F 0.8995 0.0069 0.0936 160 I 0.7981 0.0406 0.1613 161 G 0.4473 0.0307 0.5220 162 D 0.1367 0.0231 0.8402 163 S 0.0698 0.0371 0.8931 164 V 0.0137 0.6388 0.3474 165 S 0.0115 0.7376 0.2509 166 D 0.0126 0.8224 0.1650 167 E 0.0079 0.9399 0.0522 168 Q 0.0061 0.9517 0.0423 169 T 0.0054 0.9558 0.0388 170 A 0.0054 0.9537 0.0409 171 Q 0.0052 0.9482 0.0466 172 A 0.0066 0.9085 0.0850 173 A 0.0420 0.4105 0.5475 174 N 0.0485 0.0191 0.9324 175 V 0.0911 0.0078 0.9011 176 D 0.3732 0.0242 0.6026 177 F 0.9184 0.0040 0.0775 178 G 0.9257 0.0043 0.0700 179 L 0.9246 0.0035 0.0719 180 A 0.8769 0.0070 0.1161 181 V 0.6079 0.0197 0.3724 182 W 0.1668 0.0471 0.7861 183 G 0.0730 0.0751 0.8519 184 M 0.0797 0.0949 0.8255 185 D 0.0713 0.0908 0.8380 186 P 0.0633 0.1599 0.7768 187 N 0.0431 0.3382 0.6187 188 A 0.0319 0.4969 0.4712 189 D 0.0375 0.5144 0.4481 190 H 0.0552 0.4503 0.4945 191 Q 0.0604 0.3538 0.5857 192 K 0.0976 0.1721 0.7303 193 V 0.1229 0.0573 0.8198 194 A 0.3087 0.0756 0.6157 195 H 0.8270 0.0197 0.1533 196 R 0.8662 0.0118 0.1220 197 F 0.7725 0.0162 0.2113 198 Q 0.1848 0.0737 0.7415 199 K 0.1000 0.0283 0.8717 200 P 0.0084 0.8258 0.1659 201 L 0.0063 0.8936 0.1001 202 D 0.0078 0.8964 0.0958 203 I 0.0080 0.9046 0.0874 204 L 0.0067 0.8923 0.1010 205 E 0.0074 0.8296 0.1630 206 L 0.0118 0.7441 0.2441 207 F 0.0639 0.5167 0.4194 208 K 0.0210 0.2418 0.7372