# This file is the result of combining several RDB files, specifically # T0423.t06.str2.rdb (weight 1.54425) # T0423.t06.str4.rdb (weight 0.924988) # T0423.t06.pb.rdb (weight 0.789901) # T0423.t06.bys.rdb (weight 0.748322) # T0423.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 T0423.t06.str2.rdb # ============================================ # TARGET T0423 # 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 T0423.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 910.806 # # ============================================ # Comments from T0423.t06.str4.rdb # ============================================ # TARGET T0423 # 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 T0423.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 910.806 # # ============================================ # Comments from T0423.t06.pb.rdb # ============================================ # TARGET T0423 # 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 T0423.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 910.806 # # ============================================ # Comments from T0423.t06.bys.rdb # ============================================ # TARGET T0423 # 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 T0423.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 910.806 # # ============================================ # Comments from T0423.t06.alpha.rdb # ============================================ # TARGET T0423 # 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 T0423.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 910.806 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.1942 0.1478 0.6581 2 S 0.1377 0.3038 0.5585 3 D 0.1069 0.4622 0.4309 4 V 0.1198 0.5539 0.3264 5 I 0.0847 0.6732 0.2422 6 E 0.0480 0.7548 0.1973 7 G 0.0359 0.7863 0.1778 8 R 0.0431 0.7683 0.1886 9 L 0.0587 0.7447 0.1966 10 K 0.0587 0.7248 0.2165 11 E 0.0942 0.5983 0.3075 12 L 0.1525 0.3470 0.5005 13 G 0.1958 0.2128 0.5914 14 F 0.3549 0.1096 0.5355 15 T 0.3421 0.0784 0.5795 16 L 0.2579 0.0596 0.6825 17 P 0.1453 0.2220 0.6327 18 V 0.1498 0.2728 0.5773 19 A 0.1805 0.2060 0.6135 20 A 0.1741 0.2000 0.6259 21 A 0.1977 0.1543 0.6480 22 P 0.1476 0.2752 0.5772 23 A 0.1359 0.3104 0.5538 24 A 0.1808 0.2281 0.5911 25 N 0.1792 0.2091 0.6117 26 Y 0.2644 0.1572 0.5783 27 V 0.3315 0.0749 0.5936 28 P 0.3739 0.1486 0.4775 29 F 0.5639 0.1333 0.3028 30 T 0.6526 0.0969 0.2505 31 I 0.6360 0.0696 0.2944 32 S 0.4097 0.0853 0.5051 33 G 0.2041 0.0495 0.7464 34 N 0.3204 0.0460 0.6336 35 L 0.6870 0.0143 0.2987 36 L 0.7597 0.0112 0.2291 37 Y 0.7854 0.0109 0.2038 38 V 0.7377 0.0201 0.2422 39 S 0.6261 0.0407 0.3332 40 G 0.4775 0.0447 0.4778 41 Q 0.5173 0.0387 0.4439 42 L 0.4538 0.0300 0.5162 43 P 0.3501 0.0629 0.5870 44 M 0.2780 0.1220 0.6000 45 E 0.2614 0.0798 0.6587 46 S 0.1015 0.2398 0.6587 47 G 0.0708 0.1648 0.7644 48 K 0.2700 0.1278 0.6022 49 I 0.4955 0.1017 0.4028 50 A 0.4902 0.1451 0.3647 51 V 0.5296 0.1386 0.3318 52 T 0.3701 0.1234 0.5066 53 G 0.2769 0.0717 0.6514 54 L 0.4563 0.0519 0.4918 55 V 0.4651 0.0694 0.4655 56 G 0.2941 0.0922 0.6137 57 R 0.2076 0.1809 0.6116 58 D 0.1913 0.1363 0.6724 59 V 0.2728 0.0774 0.6497 60 D 0.1975 0.0354 0.7670 61 V 0.0248 0.6781 0.2971 62 A 0.0138 0.7697 0.2165 63 S 0.0176 0.8475 0.1350 64 A 0.0094 0.8786 0.1120 65 Q 0.0084 0.9139 0.0777 66 R 0.0083 0.9243 0.0675 67 A 0.0083 0.9247 0.0670 68 A 0.0083 0.9239 0.0679 69 E 0.0083 0.9244 0.0673 70 L 0.0083 0.9238 0.0679 71 C 0.0083 0.9215 0.0702 72 A 0.0083 0.9225 0.0692 73 V 0.0083 0.9194 0.0722 74 N 0.0083 0.9238 0.0680 75 I 0.0083 0.9235 0.0682 76 L 0.0083 0.9242 0.0676 77 A 0.0083 0.9243 0.0674 78 Q 0.0083 0.9234 0.0683 79 V 0.0083 0.9205 0.0711 80 K 0.0084 0.9145 0.0770 81 A 0.0094 0.8785 0.1121 82 A 0.0165 0.7890 0.1945 83 L 0.0442 0.5666 0.3892 84 N 0.0463 0.2297 0.7240 85 G 0.0622 0.1401 0.7977 86 D 0.1510 0.1690 0.6800 87 L 0.0751 0.5282 0.3967 88 S 0.0664 0.5446 0.3890 89 K 0.0901 0.5327 0.3772 90 I 0.0867 0.6405 0.2728 91 R 0.0615 0.6789 0.2596 92 R 0.1310 0.5520 0.3170 93 V 0.4420 0.2480 0.3100 94 I 0.5840 0.1271 0.2889 95 K 0.7255 0.0423 0.2322 96 L 0.7359 0.0354 0.2288 97 N 0.7170 0.0373 0.2457 98 G 0.7680 0.0198 0.2123 99 F 0.7235 0.0328 0.2437 100 V 0.6363 0.0437 0.3199 101 A 0.4304 0.0824 0.4871 102 S 0.2504 0.0620 0.6876 103 V 0.1369 0.2505 0.6126 104 P 0.0302 0.6165 0.3533 105 E 0.0371 0.6194 0.3435 106 F 0.0397 0.7129 0.2474 107 V 0.0238 0.8221 0.1541 108 E 0.0315 0.8196 0.1489 109 Q 0.0462 0.7915 0.1623 110 H 0.0516 0.7537 0.1948 111 L 0.0725 0.7311 0.1965 112 V 0.1126 0.6417 0.2457 113 I 0.1300 0.5302 0.3398 114 N 0.0937 0.4308 0.4754 115 G 0.0525 0.4484 0.4991 116 A 0.0439 0.6336 0.3225 117 S 0.0203 0.7984 0.1813 118 N 0.0121 0.8512 0.1368 119 L 0.0121 0.8772 0.1107 120 I 0.0118 0.8936 0.0947 121 A 0.0101 0.8964 0.0935 122 T 0.0127 0.8667 0.1206 123 V 0.0306 0.7236 0.2457 124 L 0.0707 0.4684 0.4609 125 G 0.0602 0.2350 0.7048 126 E 0.1329 0.1448 0.7223 127 P 0.0976 0.2029 0.6994 128 G 0.0783 0.1296 0.7921 129 R 0.1783 0.0781 0.7436 130 H 0.2189 0.1289 0.6522 131 A 0.2111 0.3618 0.4271 132 R 0.2584 0.4276 0.3140 133 A 0.3532 0.3992 0.2476 134 A 0.4080 0.3593 0.2327 135 V 0.4757 0.2828 0.2415 136 G 0.4193 0.3022 0.2785 137 M 0.3081 0.3874 0.3045 138 A 0.2332 0.3234 0.4434 139 S 0.2028 0.2345 0.5627 140 L 0.2465 0.0564 0.6971 141 P 0.1628 0.0592 0.7780 142 F 0.0721 0.3323 0.5956 143 N 0.0741 0.1599 0.7660 144 A 0.3364 0.0441 0.6195 145 S 0.6419 0.0247 0.3334 146 V 0.7776 0.0097 0.2127 147 E 0.7911 0.0078 0.2011 148 I 0.8087 0.0055 0.1858 149 D 0.7982 0.0091 0.1927 150 A 0.8185 0.0056 0.1759 151 I 0.8090 0.0066 0.1844 152 V 0.7952 0.0090 0.1958 153 E 0.7514 0.0130 0.2357 154 I 0.7118 0.0173 0.2709 155 D 0.4985 0.0340 0.4675 156 V 0.2846 0.1036 0.6119