# This file is the result of combining several RDB files, specifically # T0507.t2k.str2.rdb (weight 1.54425) # T0507.t2k.str4.rdb (weight 0.924988) # T0507.t2k.pb.rdb (weight 0.789901) # T0507.t2k.bys.rdb (weight 0.748322) # T0507.t2k.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 T0507.t2k.str2.rdb # ============================================ # TARGET T0507 # Using neural net dunbrack-40pc-3157-t2k-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 T0507.t2k-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 170.093 # # ============================================ # Comments from T0507.t2k.str4.rdb # ============================================ # TARGET T0507 # Using neural net dunbrack-40pc-3157-t2k-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 T0507.t2k-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 170.093 # # ============================================ # Comments from T0507.t2k.pb.rdb # ============================================ # TARGET T0507 # Using neural net dunbrack-40pc-3157-t2k-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 T0507.t2k-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 170.093 # # ============================================ # Comments from T0507.t2k.bys.rdb # ============================================ # TARGET T0507 # Using neural net dunbrack-40pc-3157-t2k-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 T0507.t2k-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 170.093 # # ============================================ # Comments from T0507.t2k.alpha.rdb # ============================================ # TARGET T0507 # Using neural net dunbrack-40pc-3157-t2k-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 T0507.t2k-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 170.093 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.4364 0.0343 0.5293 2 K 0.5823 0.0150 0.4027 3 V 0.7972 0.0067 0.1961 4 A 0.7460 0.0093 0.2447 5 L 0.7097 0.0286 0.2618 6 G 0.5244 0.0397 0.4359 7 G 0.3382 0.0671 0.5947 8 T 0.3247 0.1382 0.5371 9 F 0.3128 0.1961 0.4911 10 E 0.2169 0.2363 0.5468 11 P 0.0609 0.5730 0.3661 12 L 0.0559 0.5034 0.4406 13 H 0.0865 0.4548 0.4587 14 E 0.0272 0.6972 0.2757 15 G 0.0200 0.7737 0.2063 16 H 0.0111 0.8808 0.1081 17 K 0.0088 0.9011 0.0900 18 K 0.0084 0.9219 0.0698 19 L 0.0083 0.9210 0.0707 20 I 0.0083 0.9215 0.0701 21 D 0.0083 0.9246 0.0671 22 V 0.0083 0.9244 0.0673 23 A 0.0083 0.9220 0.0697 24 I 0.0084 0.9129 0.0787 25 K 0.0107 0.8195 0.1698 26 L 0.0283 0.6294 0.3423 27 G 0.0578 0.2036 0.7386 28 G 0.0877 0.0939 0.8184 29 R 0.2193 0.0719 0.7088 30 D 0.6061 0.0228 0.3711 31 I 0.7868 0.0072 0.2060 32 T 0.8093 0.0051 0.1856 33 I 0.7984 0.0072 0.1944 34 G 0.7484 0.0111 0.2404 35 V 0.6921 0.0292 0.2787 36 T 0.3166 0.0353 0.6481 37 S 0.1552 0.2038 0.6410 38 D 0.0331 0.6469 0.3200 39 R 0.0238 0.7681 0.2081 40 M 0.0217 0.8482 0.1300 41 A 0.0194 0.8529 0.1277 42 R 0.0257 0.8052 0.1691 43 A 0.0411 0.6924 0.2665 44 R 0.0904 0.4913 0.4182 45 I 0.1272 0.3310 0.5419 46 R 0.1541 0.2391 0.6068 47 S 0.1813 0.1977 0.6210 48 V 0.2485 0.1018 0.6496 49 L 0.2478 0.0598 0.6923 50 P 0.2439 0.1267 0.6293 51 F 0.2885 0.1476 0.5640 52 A 0.1648 0.4016 0.4336 53 I 0.0867 0.6596 0.2537 54 R 0.0535 0.7689 0.1776 55 A 0.0493 0.7909 0.1598 56 E 0.0434 0.7970 0.1595 57 N 0.0590 0.7559 0.1852 58 V 0.0760 0.7480 0.1760 59 K 0.1082 0.7091 0.1826 60 R 0.1807 0.6504 0.1690 61 Y 0.2709 0.5484 0.1807 62 V 0.3505 0.4321 0.2173 63 M 0.3642 0.3285 0.3074 64 R 0.3345 0.2085 0.4570 65 K 0.2807 0.1376 0.5817 66 Y 0.1959 0.1258 0.6783 67 G 0.1668 0.0882 0.7450 68 F 0.3152 0.0659 0.6189 69 E 0.4328 0.0282 0.5390 70 P 0.5067 0.0273 0.4660 71 E 0.6566 0.0238 0.3196 72 I 0.7138 0.0182 0.2680 73 V 0.6832 0.0182 0.2986 74 K 0.5856 0.0230 0.3913 75 I 0.4303 0.1062 0.4635 76 T 0.2874 0.1070 0.6056 77 N 0.2339 0.0557 0.7105 78 P 0.1075 0.3114 0.5811 79 Y 0.1267 0.1967 0.6766 80 G 0.1696 0.1173 0.7131 81 K 0.2288 0.1197 0.6515 82 T 0.2775 0.1302 0.5923 83 L 0.2505 0.1255 0.6239 84 D 0.2810 0.0813 0.6377 85 V 0.2709 0.1208 0.6083 86 D 0.2969 0.0563 0.6468 87 F 0.3568 0.0810 0.5622 88 E 0.4403 0.0616 0.4982 89 Y 0.7630 0.0103 0.2268 90 L 0.7699 0.0064 0.2237 91 V 0.7887 0.0056 0.2057 92 V 0.7217 0.0151 0.2631 93 S 0.3040 0.0165 0.6795 94 P 0.0375 0.4898 0.4727 95 E 0.0365 0.5031 0.4604 96 T 0.0972 0.4684 0.4344 97 Y 0.0636 0.6628 0.2737 98 E 0.0360 0.7385 0.2255 99 M 0.0292 0.7679 0.2029 100 A 0.0262 0.8390 0.1348 101 L 0.0153 0.8870 0.0978 102 K 0.0184 0.8802 0.1015 103 I 0.0190 0.8824 0.0986 104 N 0.0135 0.8986 0.0879 105 Q 0.0097 0.9053 0.0850 106 K 0.0106 0.9111 0.0783 107 R 0.0103 0.9119 0.0778 108 E 0.0094 0.9110 0.0796 109 E 0.0176 0.8124 0.1700 110 L 0.0563 0.4043 0.5394 111 G 0.0453 0.0721 0.8826 112 K 0.1759 0.0445 0.7797 113 R 0.2237 0.0373 0.7390 114 K 0.3524 0.0699 0.5777 115 I 0.5294 0.0309 0.4397 116 T 0.6864 0.0146 0.2991 117 I 0.7380 0.0084 0.2536 118 V 0.7453 0.0134 0.2413 119 K 0.7617 0.0066 0.2316 120 V 0.7469 0.0125 0.2406 121 D 0.7385 0.0121 0.2495 122 W 0.7491 0.0181 0.2328 123 M 0.7177 0.0227 0.2596 124 M 0.6117 0.0280 0.3603 125 A 0.3491 0.0761 0.5748 126 E 0.1706 0.2694 0.5600 127 D 0.0868 0.1486 0.7646 128 G 0.0851 0.0794 0.8355 129 K 0.2563 0.0196 0.7241 130 P 0.4623 0.0316 0.5061 131 I 0.4291 0.0677 0.5031 132 S 0.4300 0.0854 0.4846 133 S 0.4567 0.1405 0.4028 134 T 0.5645 0.1340 0.3016 135 R 0.6440 0.1004 0.2556 136 I 0.6015 0.1318 0.2667 137 K 0.4744 0.1532 0.3723 138 R 0.2663 0.1551 0.5786 139 G 0.1617 0.1193 0.7189 140 E 0.4002 0.0777 0.5221 141 I 0.5789 0.0500 0.3711 142 D 0.3984 0.0507 0.5510 143 R 0.1816 0.3623 0.4561 144 Y 0.1070 0.2225 0.6705 145 G 0.1408 0.1136 0.7456 146 G 0.2846 0.0623 0.6531 147 I 0.4701 0.0613 0.4686 148 I 0.3893 0.0685 0.5421