# This file is the result of combining several RDB files, specifically # T0309.t06.dssp-ebghstl.rdb (weight 1.53986) # T0309.t06.stride-ebghtl.rdb (weight 1.24869) # T0309.t06.str2.rdb (weight 1.54758) # T0309.t06.alpha.rdb (weight 0.659012) # T0309.t04.dssp-ebghstl.rdb (weight 1.53986) # T0309.t04.stride-ebghtl.rdb (weight 1.24869) # T0309.t04.str2.rdb (weight 1.54758) # T0309.t04.alpha.rdb (weight 0.659012) # T0309.t2k.dssp-ebghstl.rdb (weight 1.53986) # T0309.t2k.stride-ebghtl.rdb (weight 1.24869) # T0309.t2k.str2.rdb (weight 1.54758) # T0309.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 T0309.t06.dssp-ebghstl.rdb # ============================================ # TARGET T0309 # 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 T0309.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 2 # # ============================================ # Comments from T0309.t06.stride-ebghtl.rdb # ============================================ # TARGET T0309 # 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 T0309.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 2 # # ============================================ # Comments from T0309.t06.str2.rdb # ============================================ # TARGET T0309 # 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 T0309.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 2 # # ============================================ # Comments from T0309.t06.alpha.rdb # ============================================ # TARGET T0309 # 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 T0309.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 2 # # ============================================ # Comments from T0309.t04.dssp-ebghstl.rdb # ============================================ # TARGET T0309 # 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 T0309.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 2 # # ============================================ # Comments from T0309.t04.stride-ebghtl.rdb # ============================================ # TARGET T0309 # 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 T0309.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 2 # # ============================================ # Comments from T0309.t04.str2.rdb # ============================================ # TARGET T0309 # 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 T0309.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 2 # # ============================================ # Comments from T0309.t04.alpha.rdb # ============================================ # TARGET T0309 # 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 T0309.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 2 # # ============================================ # Comments from T0309.t2k.dssp-ebghstl.rdb # ============================================ # TARGET T0309 # 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 T0309.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 2 # # ============================================ # Comments from T0309.t2k.stride-ebghtl.rdb # ============================================ # TARGET T0309 # 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 T0309.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 2 # # ============================================ # Comments from T0309.t2k.str2.rdb # ============================================ # TARGET T0309 # 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 T0309.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 2 # # ============================================ # Comments from T0309.t2k.alpha.rdb # ============================================ # TARGET T0309 # 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 T0309.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 2 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.0566 0.0780 0.8654 2 A 0.1192 0.0930 0.7878 3 S 0.1305 0.0821 0.7874 4 K 0.1824 0.1306 0.6869 5 K 0.2943 0.1321 0.5736 6 V 0.4794 0.0784 0.4422 7 H 0.5830 0.0726 0.3443 8 Q 0.7466 0.0334 0.2200 9 I 0.7701 0.0226 0.2073 10 N 0.6848 0.0212 0.2941 11 V 0.5369 0.0492 0.4139 12 K 0.3456 0.0860 0.5684 13 G 0.3131 0.0864 0.6004 14 F 0.4986 0.0717 0.4297 15 F 0.5595 0.0461 0.3944 16 D 0.3977 0.0490 0.5533 17 M 0.2857 0.1866 0.5276 18 D 0.3755 0.1891 0.4353 19 V 0.5448 0.1903 0.2650 20 M 0.6185 0.1689 0.2126 21 E 0.6673 0.1301 0.2026 22 V 0.5643 0.1533 0.2824 23 T 0.3849 0.1681 0.4470 24 E 0.2038 0.2889 0.5074 25 Q 0.1746 0.2871 0.5383 26 T 0.1860 0.2267 0.5873 27 K 0.1352 0.3350 0.5298 28 E 0.2024 0.3360 0.4616 29 A 0.2458 0.3324 0.4218 30 E 0.3707 0.2368 0.3925 31 Y 0.4697 0.2056 0.3246 32 T 0.4314 0.1786 0.3900 33 Y 0.3607 0.1959 0.4433 34 D 0.2785 0.1728 0.5488 35 F 0.0155 0.9020 0.0825 36 K 0.0075 0.9360 0.0564 37 E 0.0082 0.9350 0.0568 38 I 0.0101 0.9307 0.0592 39 L 0.0142 0.8934 0.0925 40 S 0.0179 0.8396 0.1425 41 E 0.0210 0.7325 0.2465 42 F 0.0611 0.3868 0.5521 43 N 0.0487 0.1185 0.8328 44 G 0.0484 0.0622 0.8893 45 K 0.1573 0.0566 0.7861 46 N 0.4392 0.0239 0.5369 47 V 0.6720 0.0125 0.3155 48 S 0.8153 0.0077 0.1771 49 I 0.8692 0.0068 0.1240 50 T 0.8728 0.0060 0.1212 51 V 0.7929 0.0175 0.1896 52 K 0.7055 0.0358 0.2586 53 E 0.5090 0.0750 0.4160 54 E 0.3140 0.1369 0.5491 55 N 0.2686 0.1011 0.6303 56 E 0.2930 0.0708 0.6363 57 L 0.3050 0.0246 0.6704 58 P 0.3115 0.0392 0.6493 59 V 0.3283 0.0643 0.6073 60 K 0.2446 0.1381 0.6173 61 G 0.2645 0.0968 0.6386 62 V 0.5607 0.0564 0.3829 63 E 0.5913 0.0640 0.3447 64 M 0.4222 0.1052 0.4726 65 A 0.1795 0.0991 0.7214 66 G 0.0869 0.0563 0.8568 67 D 0.0991 0.0441 0.8568 68 P 0.1032 0.2130 0.6837 69 L 0.0846 0.3755 0.5399 70 E 0.0874 0.4324 0.4802 71 H 0.1045 0.3843 0.5111 72 H 0.1067 0.3260 0.5673 73 H 0.1034 0.2707 0.6258 74 H 0.1124 0.1942 0.6934 75 H 0.0919 0.1261 0.7821 76 H 0.0489 0.0484 0.9028