# This file is the result of combining several RDB files, specifically # T0437.t06.str2.rdb (weight 1.54425) # T0437.t06.str4.rdb (weight 0.924988) # T0437.t06.pb.rdb (weight 0.789901) # T0437.t06.bys.rdb (weight 0.748322) # T0437.t06.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 T0437.t06.str2.rdb # ============================================ # TARGET T0437 # Using neural net dunbrack-40pc-3157-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 T0437.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 17.3997 # # ============================================ # Comments from T0437.t06.str4.rdb # ============================================ # TARGET T0437 # Using neural net dunbrack-40pc-3157-t06-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 T0437.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 17.3997 # # ============================================ # Comments from T0437.t06.pb.rdb # ============================================ # TARGET T0437 # Using neural net dunbrack-40pc-3157-t06-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 T0437.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 17.3997 # # ============================================ # Comments from T0437.t06.bys.rdb # ============================================ # TARGET T0437 # Using neural net dunbrack-40pc-3157-t06-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 T0437.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 17.3997 # # ============================================ # Comments from T0437.t06.alpha.rdb # ============================================ # TARGET T0437 # Using neural net dunbrack-40pc-3157-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 T0437.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 17.3997 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.2128 0.1366 0.6506 2 K 0.2000 0.1604 0.6396 3 D 0.2104 0.1851 0.6045 4 V 0.2643 0.2046 0.5311 5 V 0.2823 0.2102 0.5076 6 D 0.2888 0.2069 0.5043 7 K 0.3587 0.1968 0.4445 8 C 0.3436 0.1746 0.4817 9 S 0.2722 0.1990 0.5288 10 T 0.2171 0.2171 0.5658 11 K 0.1679 0.1448 0.6873 12 G 0.1662 0.0981 0.7357 13 C 0.3432 0.0771 0.5797 14 A 0.5583 0.0696 0.3720 15 I 0.6155 0.0518 0.3328 16 D 0.5366 0.0483 0.4151 17 I 0.4625 0.1011 0.4363 18 G 0.5059 0.0643 0.4298 19 T 0.6924 0.0372 0.2704 20 V 0.7091 0.0295 0.2613 21 I 0.6580 0.0291 0.3129 22 D 0.3765 0.0406 0.5829 23 N 0.1293 0.2203 0.6504 24 D 0.1104 0.2224 0.6672 25 N 0.1955 0.1314 0.6731 26 C 0.3361 0.1121 0.5518 27 T 0.5955 0.0684 0.3361 28 S 0.7136 0.0302 0.2562 29 K 0.7617 0.0214 0.2169 30 F 0.7549 0.0268 0.2184 31 S 0.7073 0.0527 0.2400 32 R 0.6937 0.0655 0.2408 33 F 0.5737 0.1248 0.3015 34 F 0.3976 0.1511 0.4513 35 A 0.1836 0.2487 0.5677 36 T 0.1508 0.2014 0.6478 37 R 0.0136 0.7528 0.2335 38 E 0.0093 0.8701 0.1206 39 E 0.0084 0.9192 0.0723 40 A 0.0083 0.9212 0.0705 41 E 0.0084 0.9193 0.0723 42 S 0.0083 0.9233 0.0685 43 F 0.0084 0.9209 0.0708 44 M 0.0083 0.9213 0.0704 45 T 0.0083 0.9220 0.0696 46 K 0.0083 0.9224 0.0693 47 L 0.0084 0.9209 0.0707 48 K 0.0084 0.9168 0.0748 49 E 0.0083 0.9224 0.0693 50 L 0.0086 0.9132 0.0781 51 A 0.0092 0.9098 0.0810 52 A 0.0094 0.8950 0.0956 53 A 0.0155 0.8203 0.1642 54 A 0.0649 0.6117 0.3233 55 S 0.0883 0.3737 0.5380 56 S 0.1289 0.2293 0.6418 57 A 0.0831 0.3247 0.5922 58 D 0.0962 0.2409 0.6629 59 E 0.1386 0.1489 0.7125 60 G 0.1798 0.1144 0.7058 61 A 0.3747 0.0440 0.5812 62 S 0.5451 0.0262 0.4287 63 V 0.6844 0.0260 0.2896 64 A 0.6465 0.0401 0.3134 65 Y 0.6703 0.0326 0.2971 66 K 0.6711 0.0361 0.2928 67 I 0.6518 0.0407 0.3076 68 K 0.5991 0.0640 0.3370 69 D 0.5602 0.0652 0.3746 70 L 0.3735 0.2090 0.4175 71 E 0.2050 0.1691 0.6258 72 G 0.1893 0.1085 0.7023 73 Q 0.5006 0.0479 0.4516 74 V 0.7283 0.0147 0.2570 75 E 0.7802 0.0084 0.2114 76 L 0.7986 0.0087 0.1927 77 D 0.8038 0.0087 0.1876 78 A 0.8159 0.0069 0.1771 79 A 0.7962 0.0103 0.1935 80 F 0.8094 0.0081 0.1825 81 T 0.7986 0.0081 0.1934 82 F 0.7776 0.0163 0.2060 83 S 0.7322 0.0349 0.2330 84 C 0.6751 0.0712 0.2538 85 Q 0.5015 0.2213 0.2771 86 A 0.2438 0.5386 0.2176 87 E 0.1778 0.6482 0.1740 88 M 0.2360 0.6494 0.1146 89 I 0.2064 0.6870 0.1066 90 I 0.1550 0.7373 0.1077 91 F 0.1352 0.7438 0.1210 92 E 0.1756 0.6718 0.1526 93 L 0.1612 0.6432 0.1956 94 S 0.1002 0.6069 0.2928 95 L 0.0683 0.6654 0.2663 96 R 0.0794 0.6394 0.2812 97 S 0.1026 0.5987 0.2987 98 L 0.1186 0.5181 0.3634 99 A 0.1230 0.4129 0.4642