# This file is the result of combining several RDB files, specifically # T0411.t06.str2.rdb (weight 1.54425) # T0411.t06.str4.rdb (weight 0.924988) # T0411.t06.pb.rdb (weight 0.789901) # T0411.t06.bys.rdb (weight 0.748322) # T0411.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 T0411.t06.str2.rdb # ============================================ # TARGET T0411 # 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 T0411.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 5161 # # ============================================ # Comments from T0411.t06.str4.rdb # ============================================ # TARGET T0411 # 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 T0411.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 5161 # # ============================================ # Comments from T0411.t06.pb.rdb # ============================================ # TARGET T0411 # 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 T0411.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 5161 # # ============================================ # Comments from T0411.t06.bys.rdb # ============================================ # TARGET T0411 # 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 T0411.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 5161 # # ============================================ # Comments from T0411.t06.alpha.rdb # ============================================ # TARGET T0411 # 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 T0411.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 5161 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.1973 0.3550 0.4478 2 W 0.1635 0.4823 0.3542 3 K 0.1366 0.6162 0.2472 4 A 0.1713 0.6177 0.2110 5 V 0.1957 0.5979 0.2064 6 M 0.2284 0.5526 0.2190 7 N 0.2115 0.5234 0.2651 8 A 0.1604 0.5017 0.3379 9 W 0.1479 0.4046 0.4475 10 N 0.1207 0.2316 0.6476 11 G 0.1078 0.1340 0.7583 12 T 0.1573 0.1609 0.6818 13 E 0.0948 0.3941 0.5111 14 S 0.1129 0.4096 0.4775 15 Q 0.1315 0.3942 0.4743 16 S 0.1407 0.3594 0.4999 17 K 0.0819 0.4690 0.4491 18 N 0.0991 0.3779 0.5230 19 V 0.1435 0.2794 0.5772 20 S 0.1196 0.3052 0.5753 21 N 0.1240 0.2098 0.6662 22 I 0.2086 0.1305 0.6609 23 Q 0.2873 0.1229 0.5898 24 S 0.4114 0.0618 0.5268 25 Y 0.4118 0.0276 0.5606 26 S 0.1974 0.0146 0.7880 27 F 0.0184 0.7222 0.2594 28 E 0.0100 0.8616 0.1284 29 D 0.0100 0.9109 0.0791 30 M 0.0086 0.9198 0.0716 31 K 0.0084 0.9166 0.0750 32 R 0.0084 0.9140 0.0776 33 I 0.0099 0.8705 0.1196 34 V 0.0208 0.7675 0.2117 35 G 0.0241 0.5132 0.4628 36 K 0.0567 0.3554 0.5879 37 H 0.0988 0.1887 0.7125 38 D 0.1791 0.0544 0.7666 39 P 0.0884 0.3274 0.5842 40 N 0.1610 0.1297 0.7093 41 V 0.6217 0.0132 0.3651 42 V 0.7205 0.0142 0.2652 43 L 0.7629 0.0070 0.2301 44 V 0.7690 0.0124 0.2186 45 D 0.6765 0.0130 0.3105 46 V 0.4797 0.0552 0.4651 47 R 0.3079 0.0449 0.6472 48 E 0.1986 0.0230 0.7785 49 P 0.0766 0.4058 0.5175 50 S 0.0553 0.5593 0.3854 51 E 0.1189 0.5161 0.3651 52 Y 0.2152 0.4026 0.3822 53 S 0.2450 0.3490 0.4061 54 I 0.3056 0.2694 0.4249 55 V 0.3601 0.1563 0.4836 56 H 0.3855 0.0908 0.5237 57 I 0.2922 0.0504 0.6574 58 P 0.1728 0.1642 0.6630 59 A 0.1351 0.1757 0.6891 60 S 0.2929 0.1572 0.5499 61 I 0.4674 0.0884 0.4442 62 N 0.4512 0.0668 0.4820 63 V 0.3897 0.0383 0.5721 64 P 0.2520 0.0628 0.6852 65 Y 0.1561 0.2851 0.5588 66 R 0.1167 0.3258 0.5575 67 S 0.1505 0.2466 0.6029 68 H 0.1935 0.1027 0.7038 69 P 0.0627 0.4310 0.5063 70 D 0.0664 0.3409 0.5926 71 A 0.0925 0.3639 0.5436 72 F 0.1421 0.2763 0.5816 73 A 0.1824 0.2079 0.6097 74 L 0.2024 0.1195 0.6781 75 D 0.1734 0.0310 0.7956 76 P 0.0135 0.7271 0.2593 77 L 0.0101 0.8388 0.1510 78 E 0.0107 0.8973 0.0920 79 F 0.0112 0.9060 0.0828 80 E 0.0089 0.9007 0.0903 81 K 0.0093 0.8901 0.1006 82 Q 0.0156 0.8043 0.1802 83 I 0.0603 0.5256 0.4141 84 G 0.0508 0.2777 0.6715 85 I 0.1537 0.1393 0.7070 86 P 0.1548 0.1237 0.7215 87 K 0.2048 0.0643 0.7308 88 P 0.1733 0.0931 0.7335 89 D 0.1590 0.0889 0.7521 90 S 0.0490 0.3865 0.5645 91 A 0.0913 0.1910 0.7176 92 K 0.3168 0.0470 0.6362 93 E 0.5995 0.0177 0.3828 94 L 0.7850 0.0068 0.2082 95 I 0.8128 0.0052 0.1820 96 F 0.8091 0.0054 0.1855 97 Y 0.7801 0.0082 0.2117 98 C 0.5497 0.0187 0.4315 99 A 0.2454 0.1716 0.5830 100 S 0.1273 0.1744 0.6982 101 G 0.0888 0.1813 0.7299 102 K 0.1174 0.3848 0.4978 103 R 0.0877 0.5759 0.3364 104 G 0.0312 0.7926 0.1761 105 G 0.0095 0.8873 0.1032 106 E 0.0084 0.9175 0.0740 107 A 0.0083 0.9231 0.0686 108 Q 0.0083 0.9224 0.0693 109 K 0.0083 0.9242 0.0675 110 V 0.0083 0.9234 0.0683 111 A 0.0084 0.9188 0.0728 112 S 0.0088 0.9017 0.0895 113 S 0.0147 0.7610 0.2242 114 H 0.0580 0.2553 0.6867 115 G 0.0518 0.0828 0.8654 116 Y 0.1700 0.0563 0.7736 117 S 0.1642 0.2094 0.6265 118 N 0.2389 0.1230 0.6382 119 T 0.5530 0.0467 0.4003 120 S 0.6902 0.0337 0.2761 121 L 0.6772 0.0301 0.2926 122 Y 0.5358 0.0312 0.4330 123 P 0.2144 0.1518 0.6338 124 G 0.0954 0.1902 0.7144 125 S 0.1347 0.2835 0.5819 126 M 0.0594 0.6822 0.2583 127 N 0.0278 0.8077 0.1645 128 D 0.0203 0.8643 0.1154 129 W 0.0200 0.8701 0.1099 130 V 0.0231 0.8546 0.1223 131 S 0.0298 0.7048 0.2654 132 H 0.0591 0.3782 0.5627 133 G 0.0621 0.1383 0.7996 134 G 0.1267 0.0840 0.7893 135 D 0.1756 0.0738 0.7506 136 K 0.1650 0.1788 0.6562 137 L 0.1913 0.1987 0.6100 138 D 0.2220 0.1552 0.6228 139 L 0.2188 0.1913 0.5899