# This file is the result of combining several RDB files, specifically # T0581.t04.str2.rdb (weight 1.54425) # T0581.t04.str4.rdb (weight 0.924988) # T0581.t04.pb.rdb (weight 0.789901) # T0581.t04.bys.rdb (weight 0.748322) # T0581.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 T0581.t04.str2.rdb # ============================================ # TARGET T0581 # 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 T0581.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 3.21195 # # ============================================ # Comments from T0581.t04.str4.rdb # ============================================ # TARGET T0581 # 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 T0581.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 3.21195 # # ============================================ # Comments from T0581.t04.pb.rdb # ============================================ # TARGET T0581 # 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 T0581.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 3.21195 # # ============================================ # Comments from T0581.t04.bys.rdb # ============================================ # TARGET T0581 # 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 T0581.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 3.21195 # # ============================================ # Comments from T0581.t04.alpha.rdb # ============================================ # TARGET T0581 # 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 T0581.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 3.21195 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.0573 0.6947 0.2480 2 S 0.0523 0.7515 0.1962 3 R 0.0419 0.8288 0.1293 4 F 0.0537 0.8419 0.1043 5 M 0.0661 0.8329 0.1009 6 A 0.0630 0.8346 0.1024 7 L 0.0573 0.8409 0.1018 8 A 0.0938 0.7890 0.1173 9 L 0.1051 0.7510 0.1440 10 C 0.1377 0.6852 0.1770 11 F 0.1902 0.5733 0.2365 12 V 0.2026 0.4617 0.3357 13 L 0.1791 0.3076 0.5133 14 P 0.0709 0.5325 0.3966 15 T 0.0437 0.6931 0.2632 16 A 0.0483 0.7350 0.2167 17 A 0.0452 0.7757 0.1791 18 H 0.0518 0.7281 0.2201 19 A 0.0976 0.6180 0.2844 20 A 0.1544 0.4327 0.4129 21 S 0.1643 0.2293 0.6064 22 L 0.0312 0.6596 0.3092 23 K 0.0284 0.7041 0.2675 24 D 0.0342 0.7538 0.2120 25 F 0.0498 0.7703 0.1800 26 E 0.0395 0.8002 0.1604 27 L 0.0199 0.8438 0.1363 28 S 0.0121 0.8818 0.1061 29 K 0.0092 0.9083 0.0825 30 M 0.0098 0.9060 0.0842 31 L 0.0093 0.9068 0.0839 32 E 0.0088 0.9142 0.0769 33 K 0.0097 0.9104 0.0800 34 V 0.0128 0.8955 0.0917 35 A 0.0199 0.8575 0.1225 36 K 0.0246 0.8163 0.1591 37 E 0.0555 0.6311 0.3133 38 S 0.1114 0.3505 0.5381 39 S 0.0976 0.2982 0.6042 40 V 0.1125 0.2038 0.6837 41 G 0.1089 0.1201 0.7710 42 T 0.1794 0.0663 0.7543 43 P 0.1374 0.2555 0.6072 44 R 0.1215 0.4561 0.4225 45 A 0.1470 0.4699 0.3832 46 I 0.2010 0.3741 0.4249 47 N 0.1771 0.3217 0.5013 48 E 0.0315 0.6442 0.3243 49 D 0.0443 0.6900 0.2657 50 I 0.0595 0.7004 0.2401 51 L 0.0870 0.6118 0.3012 52 D 0.1074 0.5202 0.3724 53 Q 0.1428 0.2552 0.6021 54 G 0.1700 0.1182 0.7119 55 Y 0.3854 0.0620 0.5526 56 T 0.4847 0.0590 0.4563 57 V 0.4677 0.0800 0.4523 58 E 0.2840 0.1163 0.5998 59 G 0.1311 0.1585 0.7103 60 N 0.1612 0.3301 0.5087 61 Q 0.3106 0.3609 0.3286 62 L 0.3607 0.3699 0.2693 63 I 0.3870 0.3169 0.2960 64 N 0.3287 0.3066 0.3647 65 H 0.3652 0.2345 0.4002 66 L 0.4344 0.1597 0.4059 67 S 0.4459 0.1279 0.4263 68 V 0.3711 0.2387 0.3903 69 R 0.2245 0.2664 0.5092 70 A 0.0657 0.6291 0.3052 71 S 0.0324 0.7186 0.2491 72 H 0.0298 0.7745 0.1957 73 A 0.0160 0.8641 0.1199 74 E 0.0114 0.8871 0.1015 75 R 0.0154 0.8367 0.1479 76 M 0.0383 0.7252 0.2365 77 R 0.0445 0.5671 0.3884 78 S 0.0791 0.3713 0.5496 79 N 0.1654 0.1122 0.7224 80 P 0.0148 0.6829 0.3023 81 D 0.0131 0.7929 0.1940 82 S 0.0237 0.8473 0.1290 83 V 0.0237 0.8695 0.1068 84 R 0.0264 0.8563 0.1173 85 S 0.0315 0.8350 0.1334 86 Q 0.0569 0.7088 0.2343 87 L 0.0861 0.4890 0.4249 88 G 0.0810 0.3917 0.5274 89 D 0.1061 0.3657 0.5282 90 S 0.1847 0.3542 0.4611 91 V 0.2283 0.3745 0.3972 92 C 0.2374 0.3377 0.4249 93 S 0.1503 0.3709 0.4788 94 N 0.1224 0.3330 0.5446 95 T 0.0538 0.4807 0.4655 96 G 0.0540 0.5398 0.4062 97 Y 0.0287 0.8204 0.1509 98 R 0.0186 0.8886 0.0928 99 Q 0.0168 0.8971 0.0861 100 L 0.0149 0.8903 0.0948 101 L 0.0284 0.8371 0.1345 102 A 0.0394 0.7381 0.2225 103 R 0.0647 0.2896 0.6456 104 G 0.1014 0.1167 0.7819 105 A 0.3501 0.0891 0.5608 106 I 0.6675 0.0518 0.2808 107 L 0.7572 0.0277 0.2152 108 T 0.7694 0.0191 0.2114 109 Y 0.7610 0.0177 0.2213 110 S 0.7096 0.0281 0.2623 111 F 0.6470 0.0479 0.3051 112 T 0.5360 0.0702 0.3939 113 E 0.4958 0.1561 0.3482 114 Y 0.3943 0.1850 0.4207 115 K 0.3213 0.2015 0.4773 116 T 0.2565 0.1602 0.5833 117 N 0.2153 0.1056 0.6791 118 Q 0.3343 0.0579 0.6078 119 P 0.3523 0.0744 0.5733 120 V 0.3811 0.1437 0.4753 121 A 0.3544 0.1829 0.4626 122 T 0.2937 0.2705 0.4358 123 E 0.2588 0.3728 0.3684 124 R 0.2971 0.3079 0.3951 125 F 0.3276 0.2337 0.4387 126 D 0.2337 0.2374 0.5289 127 A 0.1658 0.3941 0.4401 128 G 0.1644 0.3222 0.5133 129 S 0.1857 0.2597 0.5546 130 C 0.2667 0.1785 0.5548 131 R 0.2630 0.2099 0.5272 132 I 0.2609 0.2341 0.5050 133 Q 0.1852 0.1768 0.6380 134 G 0.1189 0.1317 0.7493 135 K 0.2038 0.1145 0.6817 136 K 0.2401 0.1065 0.6534