# This file is the result of combining several RDB files, specifically # T0484.t04.str2.rdb (weight 1.54425) # T0484.t04.str4.rdb (weight 0.924988) # T0484.t04.pb.rdb (weight 0.789901) # T0484.t04.bys.rdb (weight 0.748322) # T0484.t04.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 T0484.t04.str2.rdb # ============================================ # TARGET T0484 # Using neural net dunbrack-40pc-3157-t04-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 T0484.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 24.982 # # ============================================ # Comments from T0484.t04.str4.rdb # ============================================ # TARGET T0484 # Using neural net dunbrack-40pc-3157-t04-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 T0484.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 24.982 # # ============================================ # Comments from T0484.t04.pb.rdb # ============================================ # TARGET T0484 # Using neural net dunbrack-40pc-3157-t04-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 T0484.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 24.982 # # ============================================ # Comments from T0484.t04.bys.rdb # ============================================ # TARGET T0484 # Using neural net dunbrack-40pc-3157-t04-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 T0484.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 24.982 # # ============================================ # Comments from T0484.t04.alpha.rdb # ============================================ # TARGET T0484 # Using neural net dunbrack-40pc-3157-t04-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 T0484.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 24.982 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.2061 0.1544 0.6395 2 R 0.2053 0.1770 0.6177 3 D 0.2096 0.2081 0.5823 4 M 0.1770 0.2597 0.5633 5 T 0.1481 0.2756 0.5762 6 E 0.1296 0.3846 0.4858 7 E 0.1848 0.3061 0.5091 8 T 0.1596 0.2966 0.5438 9 R 0.1206 0.3885 0.4910 10 K 0.1139 0.3547 0.5314 11 D 0.1378 0.1788 0.6833 12 L 0.2195 0.0449 0.7356 13 P 0.1563 0.0249 0.8189 14 P 0.0247 0.6721 0.3032 15 E 0.0174 0.7771 0.2055 16 A 0.0198 0.8451 0.1351 17 L 0.0223 0.8458 0.1318 18 R 0.0280 0.8413 0.1307 19 A 0.0178 0.8748 0.1074 20 L 0.0160 0.8752 0.1088 21 A 0.0199 0.8830 0.0970 22 E 0.0209 0.8659 0.1132 23 A 0.0282 0.8595 0.1123 24 E 0.0312 0.8484 0.1204 25 E 0.0233 0.8612 0.1155 26 R 0.0298 0.8338 0.1363 27 R 0.0382 0.8074 0.1544 28 R 0.0596 0.7597 0.1808 29 R 0.0453 0.7863 0.1684 30 A 0.0356 0.7926 0.1718 31 K 0.0522 0.6884 0.2593 32 A 0.0901 0.5106 0.3993 33 L 0.1448 0.2586 0.5966 34 D 0.1619 0.1537 0.6844 35 L 0.2007 0.0592 0.7401 36 P 0.1777 0.1352 0.6871 37 K 0.1813 0.3180 0.5007 38 E 0.2548 0.2705 0.4748 39 I 0.2434 0.1944 0.5622 40 G 0.1726 0.1227 0.7047 41 G 0.1919 0.0871 0.7210 42 R 0.1410 0.2224 0.6366 43 N 0.1606 0.1431 0.6963 44 G 0.1985 0.0631 0.7384 45 P 0.2309 0.0927 0.6764 46 E 0.3797 0.0496 0.5707 47 P 0.3768 0.0513 0.5718 48 V 0.4036 0.0522 0.5442 49 R 0.4283 0.0762 0.4956 50 F 0.3338 0.1070 0.5592 51 G 0.2453 0.1128 0.6419 52 D 0.2968 0.1351 0.5680 53 W 0.2278 0.3474 0.4249 54 E 0.3023 0.3334 0.3643 55 K 0.3069 0.2791 0.4140 56 K 0.2208 0.1348 0.6444 57 G 0.2441 0.0688 0.6871 58 I 0.5224 0.0475 0.4301 59 A 0.6258 0.0387 0.3355 60 I 0.6294 0.0435 0.3271 61 D 0.4970 0.0527 0.4503 62 F 0.2983 0.1457 0.5560