# This file is the result of combining several RDB files, specifically # T0396.t2k.str2.rdb (weight 1.54425) # T0396.t2k.str4.rdb (weight 0.924988) # T0396.t2k.pb.rdb (weight 0.789901) # T0396.t2k.bys.rdb (weight 0.748322) # T0396.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 T0396.t2k.str2.rdb # ============================================ # TARGET T0396 # 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 T0396.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 41.5454 # # ============================================ # Comments from T0396.t2k.str4.rdb # ============================================ # TARGET T0396 # 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 T0396.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 41.5454 # # ============================================ # Comments from T0396.t2k.pb.rdb # ============================================ # TARGET T0396 # 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 T0396.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 41.5454 # # ============================================ # Comments from T0396.t2k.bys.rdb # ============================================ # TARGET T0396 # 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 T0396.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 41.5454 # # ============================================ # Comments from T0396.t2k.alpha.rdb # ============================================ # TARGET T0396 # 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 T0396.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 41.5454 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 G 0.1504 0.1341 0.7155 2 S 0.1805 0.0881 0.7315 3 M 0.0710 0.5476 0.3814 4 L 0.0718 0.5851 0.3431 5 H 0.1045 0.4839 0.4115 6 W 0.1251 0.3316 0.5432 7 G 0.1042 0.3012 0.5946 8 P 0.0327 0.6924 0.2748 9 K 0.0189 0.7948 0.1863 10 Y 0.0134 0.8822 0.1043 11 W 0.0114 0.9096 0.0789 12 R 0.0099 0.9150 0.0752 13 S 0.0100 0.9163 0.0736 14 L 0.0109 0.9141 0.0750 15 H 0.0105 0.9140 0.0754 16 L 0.0146 0.9072 0.0782 17 Y 0.0201 0.8857 0.0942 18 A 0.0384 0.8296 0.1320 19 I 0.0809 0.6950 0.2241 20 F 0.1515 0.4225 0.4259 21 F 0.1964 0.1745 0.6290 22 S 0.0935 0.2951 0.6114 23 D 0.0808 0.2189 0.7003 24 A 0.1656 0.0841 0.7502 25 P 0.1424 0.1509 0.7067 26 S 0.1580 0.0861 0.7559 27 W 0.0239 0.6814 0.2947 28 K 0.0171 0.8178 0.1651 29 E 0.0185 0.8768 0.1047 30 K 0.0099 0.9107 0.0794 31 Y 0.0084 0.9181 0.0735 32 E 0.0083 0.9214 0.0703 33 A 0.0083 0.9201 0.0716 34 I 0.0083 0.9214 0.0703 35 Q 0.0083 0.9242 0.0675 36 W 0.0083 0.9223 0.0694 37 I 0.0084 0.9184 0.0733 38 L 0.0084 0.9123 0.0793 39 N 0.0087 0.9009 0.0904 40 F 0.0130 0.8584 0.1286 41 I 0.0160 0.8268 0.1572 42 E 0.0265 0.7443 0.2292 43 S 0.0747 0.5584 0.3669 44 L 0.1874 0.2613 0.5512 45 P 0.1286 0.3673 0.5041 46 C 0.0967 0.4969 0.4064 47 T 0.0292 0.7209 0.2499 48 R 0.0342 0.7595 0.2063 49 C 0.0381 0.8095 0.1524 50 Q 0.0128 0.8815 0.1057 51 H 0.0096 0.9022 0.0882 52 H 0.0106 0.8998 0.0896 53 A 0.0102 0.9069 0.0829 54 F 0.0088 0.9159 0.0752 55 S 0.0087 0.9140 0.0773 56 Y 0.0111 0.8877 0.1012 57 L 0.0177 0.8404 0.1419 58 T 0.0299 0.7205 0.2496 59 K 0.0657 0.4133 0.5210 60 N 0.1665 0.1323 0.7012 61 P 0.1633 0.1315 0.7052 62 L 0.2116 0.1444 0.6439 63 T 0.3269 0.1029 0.5702 64 L 0.3248 0.1282 0.5470 65 N 0.2090 0.1059 0.6851 66 N 0.1871 0.0620 0.7509 67 S 0.0397 0.5542 0.4061 68 E 0.0244 0.7266 0.2490 69 D 0.0341 0.7793 0.1866 70 F 0.0321 0.8412 0.1267 71 Q 0.0272 0.8736 0.0993 72 Y 0.0322 0.8802 0.0876 73 W 0.0327 0.8770 0.0903 74 T 0.0329 0.8666 0.1005 75 F 0.0375 0.8559 0.1066 76 A 0.0410 0.8324 0.1266 77 F 0.0417 0.7911 0.1671 78 H 0.0382 0.7479 0.2139 79 N 0.0511 0.7328 0.2161 80 N 0.0772 0.6992 0.2236 81 V 0.1202 0.6591 0.2207 82 N 0.0940 0.6507 0.2553 83 N 0.0378 0.7229 0.2393 84 R 0.0428 0.6142 0.3430 85 L 0.0778 0.2895 0.6327 86 N 0.0646 0.1187 0.8168 87 K 0.1973 0.0677 0.7350 88 K 0.2950 0.1339 0.5711 89 I 0.3979 0.1551 0.4469 90 I 0.4792 0.0928 0.4280 91 S 0.3042 0.0734 0.6224 92 W 0.1662 0.3349 0.4989 93 S 0.0902 0.5196 0.3902 94 E 0.0847 0.5929 0.3223 95 Y 0.0952 0.6502 0.2546 96 K 0.0904 0.7029 0.2067 97 N 0.0927 0.6918 0.2155 98 I 0.1165 0.6283 0.2552 99 Y 0.1555 0.5191 0.3254 100 E 0.1559 0.4266 0.4176 101 Q 0.1252 0.3273 0.5474 102 S 0.1299 0.2018 0.6682 103 I 0.1597 0.2612 0.5791 104 L 0.1708 0.2440 0.5852 105 K 0.1499 0.1806 0.6695