# This file is the result of combining several RDB files, specifically # T0500.t06.str2.rdb (weight 1.54425) # T0500.t06.str4.rdb (weight 0.924988) # T0500.t06.pb.rdb (weight 0.789901) # T0500.t06.bys.rdb (weight 0.748322) # T0500.t06.alpha.rdb (weight 0.678173) # T0500.t04.str2.rdb (weight 1.54425) # T0500.t04.str4.rdb (weight 0.924988) # T0500.t04.pb.rdb (weight 0.789901) # T0500.t04.bys.rdb (weight 0.748322) # T0500.t04.alpha.rdb (weight 0.678173) # T0500.t2k.str2.rdb (weight 1.54425) # T0500.t2k.str4.rdb (weight 0.924988) # T0500.t2k.pb.rdb (weight 0.789901) # T0500.t2k.bys.rdb (weight 0.748322) # T0500.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 T0500.t06.str2.rdb # ============================================ # TARGET T0500 # 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 T0500.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 10.4224 # # ============================================ # Comments from T0500.t06.str4.rdb # ============================================ # TARGET T0500 # 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 T0500.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 10.4224 # # ============================================ # Comments from T0500.t06.pb.rdb # ============================================ # TARGET T0500 # 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 T0500.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 10.4224 # # ============================================ # Comments from T0500.t06.bys.rdb # ============================================ # TARGET T0500 # 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 T0500.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 10.4224 # # ============================================ # Comments from T0500.t06.alpha.rdb # ============================================ # TARGET T0500 # 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 T0500.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 10.4224 # # ============================================ # Comments from T0500.t04.str2.rdb # ============================================ # TARGET T0500 # 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 T0500.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 10.902 # # ============================================ # Comments from T0500.t04.str4.rdb # ============================================ # TARGET T0500 # 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 T0500.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 10.902 # # ============================================ # Comments from T0500.t04.pb.rdb # ============================================ # TARGET T0500 # 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 T0500.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 10.902 # # ============================================ # Comments from T0500.t04.bys.rdb # ============================================ # TARGET T0500 # 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 T0500.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 10.902 # # ============================================ # Comments from T0500.t04.alpha.rdb # ============================================ # TARGET T0500 # 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 T0500.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 10.902 # # ============================================ # Comments from T0500.t2k.str2.rdb # ============================================ # TARGET T0500 # 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 T0500.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 15.3477 # # ============================================ # Comments from T0500.t2k.str4.rdb # ============================================ # TARGET T0500 # 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 T0500.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 15.3477 # # ============================================ # Comments from T0500.t2k.pb.rdb # ============================================ # TARGET T0500 # 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 T0500.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 15.3477 # # ============================================ # Comments from T0500.t2k.bys.rdb # ============================================ # TARGET T0500 # 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 T0500.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 15.3477 # # ============================================ # Comments from T0500.t2k.alpha.rdb # ============================================ # TARGET T0500 # 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 T0500.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 15.3477 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 P 0.1847 0.1304 0.6850 2 A 0.1848 0.1712 0.6440 3 R 0.2100 0.1304 0.6596 4 Q 0.2286 0.0479 0.7234 5 P 0.1963 0.0650 0.7388 6 P 0.1847 0.1629 0.6524 7 A 0.2266 0.2111 0.5623 8 A 0.2346 0.1699 0.5955 9 L 0.2456 0.1546 0.5998 10 A 0.2610 0.1027 0.6362 11 K 0.2579 0.0401 0.7020 12 P 0.2011 0.0634 0.7355 13 P 0.1734 0.1102 0.7165 14 G 0.1765 0.0859 0.7376 15 T 0.2259 0.0333 0.7407 16 P 0.1902 0.0605 0.7492 17 P 0.1701 0.2048 0.6251 18 S 0.2117 0.1778 0.6104 19 L 0.2292 0.1500 0.6209 20 G 0.2203 0.1201 0.6596 21 A 0.2373 0.1243 0.6384 22 S 0.2384 0.0464 0.7152 23 P 0.1871 0.1557 0.6573 24 A 0.2304 0.1171 0.6525 25 K 0.2590 0.0419 0.6992 26 P 0.2341 0.0453 0.7205 27 P 0.2165 0.1067 0.6768 28 S 0.2243 0.0542 0.7216 29 P 0.1541 0.1469 0.6990 30 G 0.1346 0.1167 0.7487 31 A 0.2316 0.0410 0.7274 32 P 0.2181 0.0962 0.6857 33 A 0.2615 0.1373 0.6012 34 L 0.3103 0.1005 0.5892 35 H 0.2893 0.0781 0.6326 36 V 0.2773 0.0452 0.6775 37 P 0.1981 0.1096 0.6924 38 A 0.2121 0.1254 0.6626 39 K 0.2311 0.0482 0.7207 40 P 0.1948 0.0662 0.7390 41 P 0.1629 0.1492 0.6879 42 R 0.1252 0.3605 0.5143 43 A 0.1301 0.3967 0.4732 44 A 0.1686 0.3316 0.4998 45 A 0.1823 0.2966 0.5211 46 A 0.1809 0.3069 0.5122 47 A 0.1834 0.3163 0.5003 48 A 0.2028 0.2661 0.5311 49 A 0.1822 0.2874 0.5304 50 A 0.1983 0.2291 0.5726 51 A 0.2158 0.2027 0.5815 52 A 0.2419 0.1152 0.6429 53 A 0.2567 0.0455 0.6979 54 P 0.2302 0.0555 0.7143 55 P 0.2439 0.0768 0.6793 56 A 0.2860 0.0294 0.6846 57 P 0.1922 0.0476 0.7601 58 P 0.1469 0.1944 0.6586 59 E 0.1423 0.1765 0.6812 60 G 0.1301 0.1277 0.7423 61 A 0.2011 0.0831 0.7157 62 S 0.2084 0.0523 0.7393 63 P 0.1283 0.1859 0.6858 64 G 0.1072 0.2304 0.6624 65 D 0.0999 0.4193 0.4808 66 S 0.1018 0.5895 0.3087 67 A 0.0871 0.6941 0.2189 68 R 0.1117 0.6931 0.1952 69 Q 0.1416 0.6515 0.2069 70 K 0.1459 0.5756 0.2786 71 L 0.0838 0.6777 0.2385 72 E 0.0576 0.6798 0.2626 73 E 0.0700 0.5867 0.3434 74 T 0.0894 0.5497 0.3609 75 S 0.0341 0.7717 0.1943 76 A 0.0120 0.8700 0.1180 77 C 0.0099 0.9104 0.0797 78 L 0.0087 0.9181 0.0732 79 A 0.0084 0.9198 0.0718 80 A 0.0084 0.9211 0.0706 81 A 0.0087 0.9154 0.0759 82 L 0.0091 0.9137 0.0772 83 Q 0.0087 0.9116 0.0797 84 A 0.0094 0.9036 0.0870 85 V 0.0143 0.8804 0.1052 86 E 0.0201 0.8612 0.1187 87 E 0.0296 0.8157 0.1547 88 K 0.0544 0.6980 0.2476 89 I 0.0926 0.5977 0.3098 90 R 0.1190 0.4781 0.4029 91 Q 0.1190 0.5763 0.3046 92 E 0.0966 0.5665 0.3369 93 D 0.1261 0.4328 0.4411 94 A 0.0819 0.4539 0.4642 95 Q 0.1130 0.2264 0.6606 96 G 0.1441 0.0889 0.7670 97 P 0.1337 0.1611 0.7052 98 R 0.1346 0.1864 0.6789 99 D 0.1386 0.2413 0.6201 100 S 0.1154 0.4640 0.4205 101 A 0.0980 0.6194 0.2826 102 A 0.1415 0.6163 0.2422 103 E 0.1630 0.5754 0.2615 104 K 0.1899 0.4864 0.3236 105 S 0.1839 0.3769 0.4392 106 T 0.1153 0.3675 0.5171 107 G 0.1220 0.2708 0.6072 108 S 0.1662 0.3191 0.5147 109 I 0.1611 0.4688 0.3701 110 L 0.1876 0.4982 0.3142 111 D 0.1610 0.5193 0.3197 112 D 0.1342 0.4371 0.4286 113 I 0.0810 0.4536 0.4655 114 G 0.0606 0.4333 0.5061 115 S 0.0537 0.4443 0.5021 116 M 0.0502 0.5049 0.4449 117 F 0.0511 0.5596 0.3893 118 D 0.0331 0.6515 0.3154 119 D 0.0239 0.6840 0.2920 120 L 0.0130 0.7580 0.2290 121 A 0.0093 0.8548 0.1360 122 D 0.0086 0.8777 0.1137 123 Q 0.0091 0.8738 0.1172 124 L 0.0104 0.8790 0.1106 125 D 0.0103 0.8706 0.1191 126 A 0.0134 0.7780 0.2085 127 M 0.0310 0.6421 0.3268 128 L 0.0496 0.5625 0.3878 129 E 0.0502 0.4335 0.5163