# This file is the result of combining several RDB files, specifically # T0387.t2k.str2.rdb (weight 1.54425) # T0387.t2k.str4.rdb (weight 0.924988) # T0387.t2k.pb.rdb (weight 0.789901) # T0387.t2k.bys.rdb (weight 0.748322) # T0387.t2k.alpha.rdb (weight 0.678173) # 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 T0387.t2k.str2.rdb # ============================================ # TARGET T0387 # Using neural net dunbrack-40pc-3157-t2k-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 T0387.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 317.054 # # ============================================ # Comments from T0387.t2k.str4.rdb # ============================================ # TARGET T0387 # Using neural net dunbrack-40pc-3157-t2k-IDGaaH13-3-13-7-13-9-13-11-str4-seeded.net # This is a 4-layer network, with # window units # 3 13 # 7 13 # 9 13 # 11 21 (1 str4 ) # The input amino acid frequencies were determined from # alignment T0387.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 317.054 # # ============================================ # Comments from T0387.t2k.pb.rdb # ============================================ # TARGET T0387 # Using neural net dunbrack-40pc-3157-t2k-IDGaaH13-3-13-7-13-9-13-11-pb-seeded.net # This is a 4-layer network, with # window units # 3 13 # 7 13 # 9 13 # 11 16 (1 pb ) # The input amino acid frequencies were determined from # alignment T0387.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 317.054 # # ============================================ # Comments from T0387.t2k.bys.rdb # ============================================ # TARGET T0387 # Using neural net dunbrack-40pc-3157-t2k-IDGaaH13-3-13-7-13-9-13-11-bys-seeded.net # This is a 4-layer network, with # window units # 3 13 # 7 13 # 9 13 # 11 11 (1 Bystroff ) # The input amino acid frequencies were determined from # alignment T0387.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 317.054 # # ============================================ # Comments from T0387.t2k.alpha.rdb # ============================================ # TARGET T0387 # Using neural net dunbrack-40pc-3157-t2k-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 T0387.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 317.054 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 S 0.1880 0.1185 0.6935 2 M 0.2082 0.0807 0.7111 3 K 0.3372 0.0271 0.6357 4 P 0.4486 0.0316 0.5198 5 K 0.6203 0.0303 0.3494 6 L 0.7336 0.0191 0.2473 7 C 0.7583 0.0156 0.2261 8 R 0.7848 0.0118 0.2034 9 L 0.7426 0.0196 0.2378 10 A 0.6498 0.0372 0.3130 11 K 0.4369 0.0568 0.5063 12 G 0.2099 0.0732 0.7169 13 E 0.2009 0.1710 0.6282 14 N 0.2380 0.1142 0.6478 15 G 0.3475 0.0714 0.5811 16 Y 0.5302 0.0548 0.4150 17 G 0.6187 0.0328 0.3485 18 F 0.7497 0.0146 0.2357 19 H 0.7744 0.0101 0.2155 20 L 0.7590 0.0183 0.2228 21 N 0.7128 0.0264 0.2608 22 A 0.5833 0.0614 0.3553 23 I 0.4553 0.0842 0.4604 24 R 0.2601 0.1141 0.6257 25 G 0.1410 0.1093 0.7498 26 L 0.2239 0.0411 0.7350 27 P 0.2386 0.0993 0.6621 28 G 0.3294 0.0629 0.6078 29 S 0.6134 0.0188 0.3678 30 F 0.7460 0.0118 0.2422 31 I 0.7201 0.0204 0.2595 32 K 0.6577 0.0436 0.2987 33 E 0.6849 0.0396 0.2755 34 V 0.5424 0.0614 0.3962 35 Q 0.3389 0.0624 0.5987 36 K 0.1570 0.1993 0.6436 37 G 0.0994 0.1300 0.7705 38 G 0.1629 0.1064 0.7307 39 P 0.1180 0.5409 0.3411 40 A 0.0563 0.7230 0.2207 41 D 0.0363 0.7875 0.1762 42 L 0.0737 0.6415 0.2848 43 A 0.0752 0.2480 0.6768 44 G 0.0620 0.0825 0.8555 45 L 0.2006 0.0406 0.7589 46 E 0.2020 0.0359 0.7622 47 D 0.1666 0.2042 0.6293 48 E 0.1715 0.1204 0.7081 49 D 0.3994 0.0513 0.5493 50 V 0.6873 0.0171 0.2956 51 I 0.7536 0.0115 0.2349 52 I 0.7562 0.0103 0.2335 53 E 0.7702 0.0094 0.2204 54 V 0.6461 0.0350 0.3189 55 N 0.3617 0.0493 0.5890 56 G 0.1740 0.0618 0.7642 57 V 0.4604 0.0256 0.5141 58 N 0.5342 0.0224 0.4434 59 V 0.3730 0.1133 0.5138 60 L 0.2100 0.1708 0.6192 61 D 0.1176 0.1217 0.7607 62 E 0.1860 0.0875 0.7266 63 P 0.1529 0.1579 0.6892 64 Y 0.0251 0.7122 0.2627 65 E 0.0107 0.8561 0.1332 66 K 0.0087 0.9139 0.0774 67 V 0.0086 0.9164 0.0750 68 V 0.0083 0.9218 0.0699 69 D 0.0085 0.9233 0.0682 70 R 0.0085 0.9156 0.0758 71 I 0.0110 0.8810 0.1080 72 Q 0.0150 0.7988 0.1862 73 S 0.0330 0.5931 0.3739 74 S 0.0672 0.2160 0.7167 75 G 0.0656 0.1113 0.8232 76 K 0.1661 0.0838 0.7501 77 N 0.4595 0.0323 0.5082 78 V 0.6931 0.0122 0.2947 79 T 0.7875 0.0069 0.2056 80 L 0.8142 0.0047 0.1811 81 L 0.8017 0.0060 0.1923 82 V 0.7666 0.0073 0.2261 83 C 0.6487 0.0233 0.3280 84 G 0.4268 0.0368 0.5364 85 K 0.2784 0.1218 0.5998 86 K 0.2477 0.1360 0.6163 87 A 0.1956 0.2276 0.5768 88 Q 0.1715 0.2952 0.5333 89 D 0.2271 0.1974 0.5755 90 T 0.3661 0.0978 0.5361 91 V 0.3805 0.0729 0.5466