# This file is the result of combining several RDB files, specifically # T0514.t06.str2.rdb (weight 1.54425) # T0514.t06.str4.rdb (weight 0.924988) # T0514.t06.pb.rdb (weight 0.789901) # T0514.t06.bys.rdb (weight 0.748322) # T0514.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 T0514.t06.str2.rdb # ============================================ # TARGET T0514 # 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 T0514.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 215 # # ============================================ # Comments from T0514.t06.str4.rdb # ============================================ # TARGET T0514 # 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 T0514.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 215 # # ============================================ # Comments from T0514.t06.pb.rdb # ============================================ # TARGET T0514 # 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 T0514.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 215 # # ============================================ # Comments from T0514.t06.bys.rdb # ============================================ # TARGET T0514 # 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 T0514.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 215 # # ============================================ # Comments from T0514.t06.alpha.rdb # ============================================ # TARGET T0514 # 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 T0514.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 215 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 S 0.2235 0.1240 0.6525 2 S 0.2730 0.1134 0.6136 3 L 0.3669 0.1535 0.4796 4 T 0.4071 0.1678 0.4252 5 E 0.4974 0.1350 0.3676 6 T 0.4980 0.1229 0.3791 7 Y 0.3233 0.1002 0.5765 8 G 0.2467 0.0711 0.6822 9 L 0.3995 0.0833 0.5172 10 W 0.6083 0.0631 0.3285 11 S 0.7451 0.0290 0.2259 12 I 0.7869 0.0169 0.1963 13 N 0.7573 0.0261 0.2166 14 C 0.7280 0.0325 0.2394 15 G 0.6531 0.0519 0.2950 16 I 0.5733 0.0601 0.3667 17 Q 0.3576 0.1213 0.5211 18 E 0.1341 0.1588 0.7071 19 G 0.0829 0.1049 0.8122 20 K 0.2340 0.0637 0.7023 21 K 0.4296 0.0514 0.5190 22 V 0.6395 0.0432 0.3173 23 C 0.7033 0.0391 0.2577 24 F 0.7361 0.0406 0.2233 25 M 0.7301 0.0523 0.2176 26 H 0.6938 0.0631 0.2431 27 R 0.6802 0.0415 0.2783 28 Q 0.5826 0.0450 0.3724 29 E 0.4424 0.0820 0.4756 30 V 0.3517 0.1265 0.5219 31 N 0.2099 0.1524 0.6377 32 D 0.0853 0.2787 0.6360 33 Q 0.0924 0.1771 0.7305 34 N 0.0820 0.0967 0.8214 35 R 0.3551 0.0212 0.6237 36 V 0.6485 0.0130 0.3385 37 V 0.7579 0.0087 0.2335 38 V 0.8109 0.0061 0.1831 39 A 0.8254 0.0044 0.1701 40 M 0.8311 0.0043 0.1646 41 S 0.8305 0.0044 0.1650 42 V 0.8185 0.0047 0.1768 43 V 0.8015 0.0075 0.1910 44 L 0.7479 0.0118 0.2403 45 N 0.4974 0.0175 0.4851 46 A 0.0972 0.3160 0.5868 47 D 0.0686 0.1724 0.7589 48 G 0.0821 0.0728 0.8451 49 V 0.3445 0.0393 0.6161 50 V 0.5852 0.0399 0.3749 51 S 0.6204 0.0396 0.3400 52 G 0.6964 0.0199 0.2837 53 N 0.7426 0.0111 0.2463 54 L 0.7673 0.0096 0.2231 55 T 0.7412 0.0151 0.2437 56 V 0.6125 0.0173 0.3702 57 P 0.4116 0.0444 0.5440 58 F 0.2109 0.1478 0.6413 59 G 0.2192 0.1306 0.6502 60 I 0.4510 0.0766 0.4724 61 L 0.4616 0.0627 0.4757 62 V 0.4282 0.0573 0.5145 63 S 0.2923 0.0513 0.6564 64 K 0.2676 0.1047 0.6277 65 P 0.2779 0.0908 0.6312 66 V 0.5922 0.0239 0.3839 67 R 0.7358 0.0107 0.2535 68 L 0.7819 0.0075 0.2106 69 Q 0.7804 0.0076 0.2120 70 V 0.6929 0.0124 0.2947 71 D 0.4545 0.0310 0.5145 72 E 0.1388 0.1908 0.6704 73 G 0.0849 0.1310 0.7840 74 K 0.2476 0.0915 0.6610 75 A 0.4036 0.1170 0.4794 76 V 0.5308 0.1300 0.3392 77 I 0.6236 0.0958 0.2806 78 E 0.5632 0.1019 0.3349 79 T 0.5273 0.0726 0.4002 80 G 0.4656 0.0841 0.4502 81 I 0.5266 0.0856 0.3878 82 R 0.5115 0.1103 0.3783 83 T 0.5694 0.0852 0.3454 84 C 0.4879 0.0774 0.4346 85 V 0.3730 0.0601 0.5669 86 P 0.2228 0.1772 0.5999 87 A 0.1704 0.1901 0.6395 88 G 0.2843 0.1084 0.6073 89 C 0.5613 0.0501 0.3886 90 I 0.6765 0.0377 0.2858 91 V 0.6497 0.0346 0.3157 92 P 0.5321 0.0694 0.3985 93 I 0.4920 0.0897 0.4183 94 V 0.3643 0.1152 0.5205 95 F 0.3149 0.1103 0.5748 96 D 0.1757 0.0634 0.7609 97 K 0.0124 0.7350 0.2526 98 N 0.0101 0.8575 0.1324 99 Y 0.0098 0.9105 0.0797 100 V 0.0085 0.9183 0.0732 101 A 0.0084 0.9178 0.0738 102 A 0.0086 0.9136 0.0778 103 L 0.0116 0.9003 0.0882 104 R 0.0183 0.7809 0.2007 105 A 0.0466 0.2764 0.6771 106 G 0.0582 0.1225 0.8193 107 K 0.1723 0.1270 0.7007 108 H 0.4422 0.0549 0.5029 109 L 0.6938 0.0138 0.2925 110 K 0.7822 0.0075 0.2103 111 L 0.7981 0.0055 0.1964 112 A 0.7799 0.0091 0.2110 113 M 0.7693 0.0084 0.2223 114 T 0.7107 0.0161 0.2732 115 I 0.6083 0.0335 0.3582 116 A 0.3755 0.0798 0.5447 117 A 0.2619 0.0474 0.6907 118 P 0.1288 0.1364 0.7348 119 G 0.0593 0.1057 0.8350 120 E 0.2692 0.0217 0.7092 121 P 0.4124 0.0192 0.5684 122 P 0.4167 0.0547 0.5286 123 L 0.4906 0.0647 0.4446 124 N 0.4783 0.0741 0.4476 125 D 0.5031 0.0415 0.4553 126 L 0.5754 0.0379 0.3866 127 F 0.6124 0.0301 0.3574 128 V 0.6711 0.0249 0.3040 129 Q 0.4905 0.0453 0.4642 130 L 0.2417 0.2586 0.4997 131 N 0.0957 0.3879 0.5164 132 G 0.0813 0.4096 0.5090 133 F 0.0362 0.7273 0.2365 134 S 0.0108 0.8868 0.1024 135 N 0.0086 0.9088 0.0826 136 A 0.0085 0.9129 0.0786 137 L 0.0084 0.9156 0.0760 138 N 0.0084 0.9144 0.0772 139 R 0.0085 0.9074 0.0840 140 L 0.0090 0.9018 0.0892 141 I 0.0088 0.8892 0.1020 142 A 0.0098 0.8723 0.1179 143 L 0.0242 0.7233 0.2524 144 Q 0.0673 0.4503 0.4825 145 K 0.0736 0.3172 0.6092