# This file is the result of combining several RDB files, specifically # T0327.t06.dssp-ebghstl.rdb (weight 1.53986) # T0327.t06.stride-ebghtl.rdb (weight 1.24869) # T0327.t06.str2.rdb (weight 1.54758) # T0327.t06.alpha.rdb (weight 0.659012) # T0327.t04.dssp-ebghstl.rdb (weight 1.53986) # T0327.t04.stride-ebghtl.rdb (weight 1.24869) # T0327.t04.str2.rdb (weight 1.54758) # T0327.t04.alpha.rdb (weight 0.659012) # T0327.t2k.dssp-ebghstl.rdb (weight 1.53986) # T0327.t2k.stride-ebghtl.rdb (weight 1.24869) # T0327.t2k.str2.rdb (weight 1.54758) # T0327.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 T0327.t06.dssp-ebghstl.rdb # ============================================ # TARGET T0327 # Using neural net t04-2621-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 T0327.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 4.61673 # # ============================================ # Comments from T0327.t06.stride-ebghtl.rdb # ============================================ # TARGET T0327 # 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 T0327.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 4.61673 # # ============================================ # Comments from T0327.t06.str2.rdb # ============================================ # TARGET T0327 # 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 T0327.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 4.61673 # # ============================================ # Comments from T0327.t06.alpha.rdb # ============================================ # TARGET T0327 # 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 T0327.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 4.61673 # # ============================================ # Comments from T0327.t04.dssp-ebghstl.rdb # ============================================ # TARGET T0327 # Using neural net t04-2621-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 T0327.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 4.53018 # # ============================================ # Comments from T0327.t04.stride-ebghtl.rdb # ============================================ # TARGET T0327 # 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 T0327.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 4.53018 # # ============================================ # Comments from T0327.t04.str2.rdb # ============================================ # TARGET T0327 # 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 T0327.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 4.53018 # # ============================================ # Comments from T0327.t04.alpha.rdb # ============================================ # TARGET T0327 # 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 T0327.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 4.53018 # # ============================================ # Comments from T0327.t2k.dssp-ebghstl.rdb # ============================================ # TARGET T0327 # 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 T0327.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 6 # # ============================================ # Comments from T0327.t2k.stride-ebghtl.rdb # ============================================ # TARGET T0327 # 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 T0327.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 6 # # ============================================ # Comments from T0327.t2k.str2.rdb # ============================================ # TARGET T0327 # 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 T0327.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 6 # # ============================================ # Comments from T0327.t2k.alpha.rdb # ============================================ # TARGET T0327 # 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 T0327.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 6 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.0285 0.1931 0.7784 2 N 0.0307 0.4808 0.4886 3 K 0.0114 0.7011 0.2875 4 D 0.0087 0.7948 0.1965 5 K 0.0121 0.8150 0.1729 6 L 0.0265 0.8099 0.1636 7 R 0.0306 0.8628 0.1066 8 Y 0.0542 0.8663 0.0795 9 A 0.0478 0.8735 0.0786 10 I 0.0522 0.8476 0.1002 11 L 0.0382 0.8113 0.1504 12 K 0.0585 0.5824 0.3591 13 E 0.0600 0.3276 0.6124 14 I 0.1304 0.2476 0.6220 15 F 0.1911 0.1838 0.6251 16 E 0.1178 0.1666 0.7156 17 G 0.1136 0.0857 0.8007 18 N 0.1017 0.1176 0.7807 19 T 0.1582 0.0825 0.7593 20 P 0.1768 0.0865 0.7368 21 L 0.2067 0.0448 0.7485 22 S 0.1398 0.0417 0.8186 23 E 0.0300 0.5214 0.4486 24 N 0.0188 0.4954 0.4859 25 D 0.0653 0.4980 0.4367 26 I 0.3052 0.1675 0.5273 27 G 0.3716 0.0612 0.5672 28 V 0.4803 0.0335 0.4862 29 T 0.2378 0.0359 0.7262 30 E 0.0189 0.7796 0.2015 31 D 0.0063 0.8465 0.1471 32 Q 0.0100 0.8849 0.1051 33 F 0.0049 0.9512 0.0439 34 D 0.0047 0.9564 0.0388 35 D 0.0047 0.9574 0.0379 36 A 0.0047 0.9589 0.0364 37 V 0.0047 0.9578 0.0375 38 N 0.0047 0.9550 0.0403 39 F 0.0049 0.9451 0.0500 40 L 0.0066 0.9387 0.0547 41 K 0.0087 0.8623 0.1290 42 R 0.0122 0.6725 0.3153 43 E 0.0447 0.1279 0.8274 44 G 0.0418 0.0267 0.9315 45 Y 0.2718 0.0222 0.7060 46 I 0.7881 0.0068 0.2051 47 I 0.7949 0.0300 0.1751 48 G 0.8606 0.0121 0.1273 49 V 0.8664 0.0084 0.1252 50 H 0.8516 0.0064 0.1419 51 Y 0.6763 0.0136 0.3101 52 S 0.2811 0.0473 0.6716 53 D 0.0949 0.0636 0.8415 54 D 0.0824 0.0680 0.8496 55 R 0.2014 0.0305 0.7681 56 P 0.4122 0.0400 0.5479 57 H 0.6666 0.0434 0.2900 58 L 0.7470 0.0472 0.2058 59 Y 0.7128 0.0518 0.2354 60 K 0.6068 0.0701 0.3231 61 L 0.2981 0.0955 0.6064 62 G 0.1956 0.0590 0.7454 63 P 0.2778 0.1124 0.6097 64 E 0.5672 0.1195 0.3133 65 L 0.5295 0.1468 0.3237 66 T 0.3937 0.1877 0.4186 67 E 0.1046 0.6299 0.2655 68 K 0.0328 0.6288 0.3384 69 G 0.0210 0.6853 0.2938 70 E 0.0082 0.8941 0.0977 71 N 0.0091 0.9074 0.0835 72 Y 0.0090 0.8870 0.1040 73 L 0.0172 0.8440 0.1387 74 K 0.0156 0.7892 0.1951 75 E 0.0146 0.6966 0.2888 76 N 0.0405 0.5800 0.3795 77 G 0.0149 0.7558 0.2293 78 T 0.0109 0.8308 0.1583 79 W 0.0065 0.9262 0.0673 80 S 0.0060 0.9455 0.0485 81 K 0.0059 0.9465 0.0476 82 A 0.0054 0.9508 0.0439 83 Y 0.0057 0.9487 0.0456 84 K 0.0060 0.9438 0.0502 85 T 0.0060 0.9374 0.0565 86 I 0.0072 0.9358 0.0570 87 K 0.0072 0.9315 0.0612 88 E 0.0093 0.9142 0.0765 89 I 0.0113 0.8842 0.1045 90 K 0.0122 0.8590 0.1288 91 D 0.0199 0.7484 0.2317 92 W 0.0390 0.6586 0.3023 93 I 0.1324 0.2765 0.5910 94 K 0.1462 0.1667 0.6871 95 L 0.0998 0.3867 0.5135 96 E 0.1042 0.3762 0.5196 97 H 0.0990 0.3720 0.5290 98 H 0.0964 0.3173 0.5863 99 H 0.0963 0.2375 0.6662 100 H 0.0965 0.1673 0.7362 101 H 0.0879 0.1062 0.8059 102 H 0.0496 0.0465 0.9038