# This file is the result of combining several RDB files, specifically # T0429.t06.str2.rdb (weight 1.54425) # T0429.t06.str4.rdb (weight 0.924988) # T0429.t06.pb.rdb (weight 0.789901) # T0429.t06.bys.rdb (weight 0.748322) # T0429.t06.alpha.rdb (weight 0.678173) # T0429.t04.str2.rdb (weight 1.54425) # T0429.t04.str4.rdb (weight 0.924988) # T0429.t04.pb.rdb (weight 0.789901) # T0429.t04.bys.rdb (weight 0.748322) # T0429.t04.alpha.rdb (weight 0.678173) # T0429.t2k.str2.rdb (weight 1.54425) # T0429.t2k.str4.rdb (weight 0.924988) # T0429.t2k.pb.rdb (weight 0.789901) # T0429.t2k.bys.rdb (weight 0.748322) # T0429.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 T0429.t06.str2.rdb # ============================================ # TARGET T0429 # 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 T0429.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 8.68398 # # ============================================ # Comments from T0429.t06.str4.rdb # ============================================ # TARGET T0429 # 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 T0429.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 8.68398 # # ============================================ # Comments from T0429.t06.pb.rdb # ============================================ # TARGET T0429 # 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 T0429.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 8.68398 # # ============================================ # Comments from T0429.t06.bys.rdb # ============================================ # TARGET T0429 # 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 T0429.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 8.68398 # # ============================================ # Comments from T0429.t06.alpha.rdb # ============================================ # TARGET T0429 # 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 T0429.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 8.68398 # # ============================================ # Comments from T0429.t04.str2.rdb # ============================================ # TARGET T0429 # 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 T0429.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 8.69522 # # ============================================ # Comments from T0429.t04.str4.rdb # ============================================ # TARGET T0429 # 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 T0429.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 8.69522 # # ============================================ # Comments from T0429.t04.pb.rdb # ============================================ # TARGET T0429 # 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 T0429.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 8.69522 # # ============================================ # Comments from T0429.t04.bys.rdb # ============================================ # TARGET T0429 # 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 T0429.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 8.69522 # # ============================================ # Comments from T0429.t04.alpha.rdb # ============================================ # TARGET T0429 # 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 T0429.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 8.69522 # # ============================================ # Comments from T0429.t2k.str2.rdb # ============================================ # TARGET T0429 # 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 T0429.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 7.11429 # # ============================================ # Comments from T0429.t2k.str4.rdb # ============================================ # TARGET T0429 # 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 T0429.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 7.11429 # # ============================================ # Comments from T0429.t2k.pb.rdb # ============================================ # TARGET T0429 # 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 T0429.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 7.11429 # # ============================================ # Comments from T0429.t2k.bys.rdb # ============================================ # TARGET T0429 # 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 T0429.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 7.11429 # # ============================================ # Comments from T0429.t2k.alpha.rdb # ============================================ # TARGET T0429 # 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 T0429.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 7.11429 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.2924 0.1436 0.5640 2 H 0.2387 0.1404 0.6209 3 H 0.2363 0.1782 0.5855 4 H 0.2061 0.2054 0.5884 5 H 0.2167 0.1827 0.6006 6 H 0.2235 0.1706 0.6059 7 H 0.1860 0.1638 0.6502 8 S 0.1482 0.2602 0.5916 9 S 0.1168 0.2180 0.6653 10 G 0.1060 0.1498 0.7442 11 R 0.2112 0.1170 0.6719 12 E 0.2122 0.2440 0.5437 13 N 0.2155 0.2531 0.5313 14 L 0.2027 0.3220 0.4753 15 Y 0.2078 0.3058 0.4865 16 F 0.2001 0.3308 0.4691 17 Q 0.1652 0.2883 0.5464 18 G 0.1482 0.2413 0.6105 19 M 0.2192 0.2214 0.5594 20 W 0.2534 0.2493 0.4973 21 D 0.2423 0.2485 0.5092 22 E 0.2429 0.1910 0.5661 23 T 0.1315 0.3762 0.4923 24 E 0.1712 0.2975 0.5313 25 L 0.2791 0.1938 0.5271 26 G 0.3552 0.1271 0.5177 27 L 0.5794 0.0938 0.3268 28 Y 0.6501 0.0571 0.2928 29 K 0.6557 0.0558 0.2885 30 V 0.4992 0.1110 0.3897 31 N 0.3094 0.1340 0.5566 32 E 0.3172 0.1915 0.4913 33 Y 0.4217 0.1511 0.4272 34 V 0.5346 0.0721 0.3933 35 D 0.3876 0.0524 0.5600 36 A 0.1874 0.4046 0.4080 37 R 0.1557 0.3709 0.4734 38 D 0.1766 0.3001 0.5233 39 T 0.0953 0.4373 0.4674 40 N 0.1040 0.3741 0.5219 41 M 0.1265 0.3150 0.5584 42 G 0.1846 0.2238 0.5916 43 A 0.3347 0.2753 0.3900 44 W 0.5118 0.2033 0.2849 45 F 0.6385 0.1377 0.2238 46 E 0.6586 0.1139 0.2275 47 A 0.7334 0.0547 0.2119 48 Q 0.7310 0.0565 0.2124 49 V 0.6637 0.0582 0.2781 50 V 0.5646 0.1076 0.3279 51 R 0.5960 0.0891 0.3149 52 V 0.4737 0.1318 0.3945 53 T 0.4084 0.1218 0.4698 54 R 0.2892 0.1999 0.5109 55 K 0.2617 0.1410 0.5973 56 A 0.2257 0.0644 0.7099 57 P 0.1428 0.2104 0.6468 58 S 0.1554 0.1799 0.6646 59 R 0.1260 0.2427 0.6313 60 D 0.1405 0.1426 0.7169 61 E 0.2230 0.0746 0.7023 62 P 0.1946 0.1375 0.6679 63 C 0.2417 0.1317 0.6266 64 S 0.1884 0.1448 0.6668 65 S 0.1559 0.2107 0.6334 66 T 0.1457 0.2414 0.6128 67 S 0.1712 0.1541 0.6747 68 R 0.2404 0.0842 0.6755 69 P 0.2016 0.1604 0.6380 70 A 0.2380 0.1563 0.6057 71 L 0.2109 0.1962 0.5929 72 E 0.1717 0.3108 0.5176 73 E 0.1901 0.2896 0.5204 74 D 0.3680 0.1355 0.4965 75 V 0.6031 0.0504 0.3464 76 I 0.7115 0.0216 0.2669 77 Y 0.7843 0.0105 0.2052 78 H 0.7903 0.0070 0.2027 79 V 0.7791 0.0083 0.2126 80 K 0.7120 0.0127 0.2753 81 Y 0.5650 0.0436 0.3913 82 D 0.2956 0.1604 0.5440 83 D 0.2243 0.1672 0.6085 84 Y 0.2460 0.0596 0.6943 85 P 0.1535 0.2360 0.6106 86 E 0.1052 0.2954 0.5994 87 N 0.1615 0.1424 0.6961 88 G 0.2489 0.0739 0.6772 89 V 0.5621 0.0365 0.4014 90 V 0.6792 0.0231 0.2977 91 Q 0.7284 0.0175 0.2541 92 M 0.6676 0.0252 0.3072 93 N 0.3972 0.0285 0.5743 94 S 0.2229 0.2492 0.5279 95 R 0.1214 0.3602 0.5184 96 D 0.1653 0.2286 0.6061 97 V 0.2592 0.1728 0.5680 98 R 0.3072 0.1413 0.5515 99 A 0.1550 0.5236 0.3214 100 R 0.1463 0.5386 0.3151 101 A 0.1167 0.6549 0.2284 102 R 0.1428 0.5916 0.2656 103 T 0.2772 0.4682 0.2546 104 I 0.3608 0.3054 0.3338 105 I 0.4951 0.1596 0.3453 106 K 0.3499 0.1449 0.5052 107 W 0.1966 0.3513 0.4521 108 Q 0.1298 0.3590 0.5112 109 D 0.1907 0.2083 0.6010 110 L 0.3251 0.0712 0.6036 111 E 0.2974 0.0672 0.6353 112 V 0.3184 0.0991 0.5824 113 G 0.3108 0.0634 0.6258 114 Q 0.5005 0.0238 0.4757 115 V 0.7429 0.0083 0.2487 116 V 0.8010 0.0079 0.1911 117 M 0.7932 0.0072 0.1996 118 L 0.7664 0.0206 0.2131 119 N 0.6657 0.0255 0.3088 120 Y 0.4135 0.0553 0.5312 121 N 0.2475 0.0266 0.7258 122 P 0.0467 0.4417 0.5116 123 D 0.0691 0.3056 0.6253 124 N 0.1930 0.1140 0.6930 125 P 0.1216 0.3318 0.5466 126 K 0.0939 0.4142 0.4918 127 E 0.1824 0.3693 0.4484 128 R 0.2251 0.1387 0.6362 129 G 0.2538 0.0737 0.6726 130 F 0.5368 0.0399 0.4234 131 W 0.6805 0.0437 0.2759 132 Y 0.6578 0.0549 0.2873 133 D 0.5600 0.0819 0.3581 134 A 0.4206 0.3083 0.2711 135 E 0.4716 0.2939 0.2346 136 I 0.4719 0.3298 0.1983 137 S 0.3528 0.4130 0.2342 138 R 0.3413 0.4086 0.2501 139 K 0.2780 0.4051 0.3168 140 R 0.2600 0.3334 0.4066 141 E 0.2153 0.2871 0.4977 142 T 0.2070 0.2166 0.5764 143 R 0.2193 0.2207 0.5599 144 T 0.2504 0.1859 0.5637 145 A 0.1489 0.4356 0.4155 146 R 0.1701 0.4866 0.3434 147 E 0.3935 0.2958 0.3107 148 L 0.5454 0.1715 0.2831 149 Y 0.6454 0.0942 0.2605 150 A 0.6862 0.0712 0.2425 151 N 0.7081 0.0519 0.2399 152 V 0.7395 0.0351 0.2255 153 V 0.6818 0.0363 0.2819 154 L 0.5410 0.0511 0.4079 155 G 0.2266 0.0647 0.7086 156 D 0.1535 0.1442 0.7023 157 D 0.1241 0.2182 0.6577 158 S 0.1800 0.2001 0.6199 159 L 0.1950 0.2223 0.5827 160 N 0.1600 0.2393 0.6007 161 D 0.1509 0.1641 0.6849 162 C 0.3657 0.0896 0.5447 163 R 0.5690 0.0538 0.3772 164 I 0.6682 0.0451 0.2867 165 I 0.6623 0.0502 0.2875 166 F 0.5466 0.0802 0.3732 167 V 0.3010 0.3493 0.3497 168 D 0.2698 0.4112 0.3191 169 E 0.2955 0.4107 0.2938 170 V 0.4364 0.2991 0.2645 171 F 0.5764 0.1773 0.2463 172 K 0.6174 0.1261 0.2565 173 I 0.5757 0.1014 0.3230 174 E 0.4282 0.0947 0.4771 175 R 0.3096 0.0522 0.6382 176 P 0.1712 0.1251 0.7037 177 G 0.1011 0.1083 0.7905 178 E 0.2196 0.0976 0.6828