# 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 322.136 # # ============================================ # 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 322.136 # # ============================================ # 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 322.136 # # ============================================ # 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 322.136 # # ============================================ # 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 322.136 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 S 0.1883 0.1180 0.6936 2 M 0.2090 0.0802 0.7108 3 K 0.3380 0.0269 0.6351 4 P 0.4502 0.0307 0.5191 5 K 0.6219 0.0299 0.3482 6 L 0.7348 0.0187 0.2465 7 C 0.7587 0.0155 0.2258 8 R 0.7853 0.0115 0.2032 9 L 0.7428 0.0193 0.2380 10 A 0.6493 0.0368 0.3139 11 K 0.4354 0.0564 0.5082 12 G 0.2090 0.0736 0.7174 13 E 0.2010 0.1707 0.6283 14 N 0.2392 0.1139 0.6469 15 G 0.3479 0.0714 0.5806 16 Y 0.5310 0.0547 0.4143 17 G 0.6190 0.0329 0.3481 18 F 0.7501 0.0146 0.2353 19 H 0.7744 0.0101 0.2155 20 L 0.7590 0.0184 0.2226 21 N 0.7134 0.0261 0.2606 22 A 0.5835 0.0613 0.3552 23 I 0.4553 0.0843 0.4604 24 R 0.2599 0.1140 0.6261 25 G 0.1407 0.1095 0.7498 26 L 0.2241 0.0410 0.7350 27 P 0.2388 0.0987 0.6624 28 G 0.3292 0.0627 0.6080 29 S 0.6130 0.0187 0.3684 30 F 0.7458 0.0118 0.2424 31 I 0.7201 0.0203 0.2597 32 K 0.6573 0.0434 0.2993 33 E 0.6847 0.0396 0.2757 34 V 0.5410 0.0611 0.3979 35 Q 0.3380 0.0624 0.5996 36 K 0.1571 0.1991 0.6438 37 G 0.0994 0.1302 0.7705 38 G 0.1628 0.1064 0.7308 39 P 0.1180 0.5406 0.3414 40 A 0.0563 0.7230 0.2207 41 D 0.0364 0.7872 0.1763 42 L 0.0739 0.6414 0.2848 43 A 0.0752 0.2480 0.6768 44 G 0.0624 0.0826 0.8550 45 L 0.2006 0.0406 0.7588 46 E 0.2019 0.0359 0.7622 47 D 0.1665 0.2044 0.6290 48 E 0.1712 0.1203 0.7086 49 D 0.3994 0.0511 0.5495 50 V 0.6876 0.0171 0.2953 51 I 0.7536 0.0115 0.2350 52 I 0.7563 0.0103 0.2334 53 E 0.7703 0.0094 0.2203 54 V 0.6460 0.0350 0.3189 55 N 0.3617 0.0493 0.5891 56 G 0.1744 0.0617 0.7639 57 V 0.4603 0.0256 0.5141 58 N 0.5340 0.0222 0.4438 59 V 0.3732 0.1130 0.5138 60 L 0.2102 0.1706 0.6191 61 D 0.1177 0.1212 0.7611 62 E 0.1863 0.0867 0.7270 63 P 0.1532 0.1564 0.6904 64 Y 0.0250 0.7123 0.2628 65 E 0.0106 0.8561 0.1333 66 K 0.0088 0.9138 0.0775 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 0.8808 0.1081 72 Q 0.0150 0.7985 0.1865 73 S 0.0331 0.5923 0.3746 74 S 0.0671 0.2155 0.7174 75 G 0.0655 0.1111 0.8233 76 K 0.1664 0.0838 0.7499 77 N 0.4606 0.0322 0.5072 78 V 0.6936 0.0122 0.2942 79 T 0.7875 0.0070 0.2055 80 L 0.8141 0.0047 0.1811 81 L 0.8017 0.0060 0.1923 82 V 0.7666 0.0073 0.2261 83 C 0.6485 0.0235 0.3280 84 G 0.4264 0.0367 0.5369 85 K 0.2766 0.1239 0.5995 86 K 0.2461 0.1399 0.6140 87 A 0.1953 0.2322 0.5726 88 Q 0.1706 0.3023 0.5271 89 D 0.2265 0.2033 0.5702 90 T 0.3703 0.0986 0.5311 91 V 0.3848 0.0710 0.5442