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2 additions
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107 deletions
| ... | @@ -6,4 +6,4 @@ GGACAUACAAUCGCGUGGAUAUGGCACGCAAGUUUCUGCCGGGCACCGUAAAUGUCCGACUAUGUCCa | ... | @@ -6,4 +6,4 @@ GGACAUACAAUCGCGUGGAUAUGGCACGCAAGUUUCUGCCGGGCACCGUAAAUGUCCGACUAUGUCCa |
| 6 | (((((((...(((((((.[[..[[)))))))........((((((]]...]]))))))..))))))). | 6 | (((((((...(((((((.[[..[[)))))))........((((((]]...]]))))))..))))))). |
| 7 | >__'SOLUTION_STRUCTURE_OF_THE_P2B-P3_PSEUDOKNOT_FROM_HUMAN_TELOMERASE_RNA_'_(PDB_00857) | 7 | >__'SOLUTION_STRUCTURE_OF_THE_P2B-P3_PSEUDOKNOT_FROM_HUMAN_TELOMERASE_RNA_'_(PDB_00857) |
| 8 | GGGCUGUUUUUCUCGCUGACUUUCAGCCCCAAACAAAAAAGUCAGCA | 8 | GGGCUGUUUUUCUCGCUGACUUUCAGCCCCAAACAAAAAAGUCAGCA |
| 9 | -[[[[[[........(((((((((]]]]]]........))))))))). | ||
| ... | \ No newline at end of file | ... | \ No newline at end of file |
| 9 | +[[[[[[........(((((((((]]]]]]........))))))))). | ... | ... |
data/sec_structs/verified_tRNAs.dbn
deleted
100644 → 0
| 1 | ->>__'CRYSTAL_STRUCTURE_ANALYSIS_OF_A_TRNA-NEOMYCIN_COMPLEX_'_(PDB_00095) | ||
| 2 | -GCGGAUUUAGCUCAGUUGGGAGAGCGCCAGACUGAAGACUGGAGGUCCUGUGUUCGAUCCACAGAAUUCGCACCA | ||
| 3 | -(((((((..((((........))))(((((........)))))....(((((.......)))))))))))).... | ||
| 4 | ->>__'YEAST_INITIATOR_TRNA_'_(PDB_00229) | ||
| 5 | -AGCGCCGUGGCGCAGUGGAAGCGCGCAGGGCUCAUAACCCUGAUGUCCUCGGAUCGAAACCGAGCGGCGCUACCA | ||
| 6 | -(((((((..((((.......))))(((((((.....)))))))....(((((.......)))))))))))).... | ||
| 7 | ->>__'THE_CRYSTAL_STRUCTURE_OF_PHENYLALANYL-TRNA_SYNTHETASE_FROM_THERMUS_THERMOPHILUS_COMPLEXED_WITH_COGNATE_TRNAPHE_'_(PDB_00362) | ||
| 8 | -GCCGAGGUAGCUCAGUUGGUAGAGCAUGCGACUGAAAAUCGCAGUGUCCGCGGUUCGAUUCCGCGCCUCGGCACCA | ||
| 9 | -(((((((..((((........))))((((((.......))))))....(((((.......)))))))))))).... | ||
| 10 | ->>__'CRYSTAL_STRUCTURE_OF_GLUTAMINYL-TRNA_SYNTHETASE_COMPLEXED_WITH_A_TRNA-GLN_MUTANT_AND_AN_ACTIVE-SITE_INHIBITOR_'_(PDB_00373) | ||
| 11 | -GGGGUAUCGCCAAGCGGUAAGGCACCGGAUUCUGAUUCCGGCAGCGAGGUUCGAAUCCUCGUACCCCAGCCA | ||
| 12 | -((((((..((((.......))))((((((((...))))))))..(((((.......)))))))))))..... | ||
| 13 | ->>__'GLUTAMINYL-TRNA_SYNTHETASE_COMPLEXED_WITH_A_TRNA_MUTANT_AND_AN_ACTIVE_SITE_INHIBITOR_'_(PDB_00374) | ||
| 14 | -GGGGUAUCGCCAAGCGGUAAGGCACCGGAUUCUGAUUCCGGCAAGCGAGGUUCGAAUCCUCGUACCCCAGCCA | ||
| 15 | -((((((..((((.......))))((((((((...))))))))...(((((.......)))))))))))..... | ||
| 16 | ->>__'CRYSTAL_STRUCTURE_OF_A_TIGHT-BINDING_GLUTAMINE_TRNA_BOUND_TO_GLUTAMINE_AMINOACYL_TRNA_SYNTHETASE_'_(PDB_00376) | ||
| 17 | -GGGGUAUCGCCAAGCGGUAAGGCACCGGAUUCUGAUUCCGGAGGUCGAGGUUCGAAUCCUCGUACCCCAGCCA | ||
| 18 | -((((((..(((.........)))((((((((...))))))))...(((((.......)))))))))))..... | ||
| 19 | ->>__'INSIGHTS_INTO_EDITING_FROM_AN_ILE-TRNA_SYNTHETASE_STRUCTURE_WITH_TRNA(ILE)_AND_MUPIROCIN_'_(PDB_00402) | ||
| 20 | -GGGCUUGUAGCUCAGGUGGUUAGAGCGCACCCCUGAUAAGGGUGAGGUCGGUGGUUCAAGUCCACUCAGGCCCAC | ||
| 21 | -(((((((..((((.........))))(((((((.....)))))))....(((((.......)))))))))))).. | ||
| 22 | ->>__'STRUCTURAL_BASIS_OF_ANTICODON_LOOP_RECOGNITION_BY_GLUTAMINYL-TRNA_SYNTHETASE_'_(PDB_00425) | ||
| 23 | -GGGGUAUCGCCAAGCGGUAAGGCACCGGAUUCUGAUUCCGGCAUUCCGAGGUUCGAAUCCUCGUACCCCAGCCA | ||
| 24 | -((((((..(((.........)))((((((((...))))))))....(((((.......)))))))))))..... | ||
| 25 | ->>__'STRUCTURAL_BASIS_FOR_TRANSFER_RNA_AMINOACEYLATION_BY_ESCHERICHIA_COLI_GLUTAMINYL-TRNA_SYNTHETASE_'_(PDB_00426) | ||
| 26 | -GGGGUAUCGCCAAGCGGUAAGGCACCGGAUUCUGAUUCCGGCAUUCCGAGGUUCGAAUCCUCGUACCCCAGCCA | ||
| 27 | -((((((..(((.........))).(((((((...))))))).....(((((.......)))))))))))..... | ||
| 28 | ->>__'CRYSTAL_STRUCTURE_OF_ARCHAEAL_TYROSYL-TRNA_SYNTHETASE_COMPLEXED_WITH_TRNA(TYR)_AND_L-TYROSINE_'_(PDB_00474) | ||
| 29 | -CCGGCGGUAGUUCAGCCUGGUAGAACGGCGGACUGUAGAUCCGCAUGUCGCUGGUUCAAAUCCGGCCCGCCGGA | ||
| 30 | -(((((((..((((.........))))(((((((.....)))))))....(((((.......)))))))))))). | ||
| 31 | ->>__'CRYSTAL_STRUCTURE_OF_L-GLUTAMINE_AND_AMPCPP_BOUND_TO_GLUTAMINE_AMINOACYL_TRNA_SYNTHETASE_'_(PDB_00620) | ||
| 32 | -GGGGUAUCGCCAAGCGGUAAGGCACCGGAUUCUGAUUCCGGCAUUCCGAGGUUCGAAUCCUCGUACCCCAGCCA | ||
| 33 | -((((((..((((.......))))(((((((.....)))))))....(((((.......)))))))))))..... | ||
| 34 | ->>__'CRYSTAL_STRUCTURE_OF_L-GLUTAMATE_AND_AMPCPP_BOUND_TO_GLUTAMINE_AMINOACYL_TRNA_SYNTHETASE_'_(PDB_00621) | ||
| 35 | -GGGGUAUCGCCAAGCGGUAAGGCACCGGAUUCUGAUUCCGGCAUUCCGAGGUUCGAAUCCUCGUACCCCAGCCA | ||
| 36 | -((((((..((((.......)))).(((((((...))))))).....(((((.......)))))))))))..... | ||
| 37 | ->>__'CRYSTAL_STRUCTURE_OF_THE_TRNA_DOMAIN_OF_TRANSFER-MESSENGER_RNA_IN_COMPLEX_WITH_SMPB_'_(PDB_00637) | ||
| 38 | -GAUUCGACGGGGACUUCGGUCCUCGGACGCGGGUUCGAUUCCCGCUCGACGGGGACUUCGGUCCUCGGA | ||
| 39 | -......((((((((....))))))))..(((((.......)))))...((((((((....)))))))). | ||
| 40 | ->>__'GLUTAMINYL-TRNA_SYNTHETASE_MUTANT_D235N_COMPLEXED_WITH_GLUTAMINE_TRANSFER_RNA_'_(PDB_00669) | ||
| 41 | -GGGGUAUCGCCAAGCGGUAAGGCACCGGAUUCUGAUUCCGGCAUUCCGAGGUUCGAAUCCUCGUACCCCAGCCA | ||
| 42 | -((((((..(((.........)))((((((((...))))))))....(((((.......)))))))))))..... | ||
| 43 | ->>__'GLUTAMINYL-TRNA_SYNTHETASE_MUTANT_D235G_COMPLEXED_WITH_GLUTAMINE_TRANSFER_RNA_'_(PDB_00670) | ||
| 44 | -GGGGUAUCGCCAAGCGGUAAGGCACCGGAUUCUGAUUCCGGCAUUCCGAGGUUCGAAUCCUCGUACCCCAGCCA | ||
| 45 | -((((((..(((.........)))(((((((.....)))))))....(((((.......)))))))))))..... | ||
| 46 | ->>__'GLUTAMINYL-TRNA_SYNTHETASE_MUTANT_I129T_COMPLEXED_WITH_GLUTAMINE_TRANSFER_RNA_'_(PDB_00671) | ||
| 47 | -GGGGUAUCGCCAAGCGGUAAGGCACCGGAUUCUGAUUCCGGCAUUCCGAGGUUCGAAUCCUCGUACCCCAGCCA | ||
| 48 | -((((((..(((.........)))((((((.......))))))....(((((.......)))))))))))..... | ||
| 49 | ->>__'GLUTAMINYL-TRNA_SYNTHETASE_COMPLEXED_WITH_TRNA_AND_AN_AMINO_ACID_ANALOG_'_(PDB_00672) | ||
| 50 | -GGGGUAUCGCCAAGCGGUAAGGCACCGGAUUCUGAUUCCGGCAUUCCGAGGUUCGAAUCCUCGUACCCCAGCCA | ||
| 51 | -((((((..((((.......))))((((((((...))))))))....(((((.......)))))))))))..... | ||
| 52 | ->>__'INSIGHTS_INTO_EDITING_FROM_AN_ILE-TRNA_SYNTHETASE_STRUCTURE_WITH_TRNA(ILE)_AND_MUPIROCIN_'_(PDB_00673) | ||
| 53 | -GGGCUUGUAGCUCAGGUGGUUAGAGCGCACCCCUGAUAAGGGUGAGGUCGGUGGUUCAAGUCCACUCAGGCCCAC | ||
| 54 | -(((((((..((((.........))))(((((((.....)))))))....(((((.......)))))))))))).. | ||
| 55 | ->>__'INSIGHTS_INTO_EDITING_FROM_AN_ILE-TRNA_SYNTHETASE_STRUCTURE_WITH_TRNA(ILE)_AND_MUPIROCIN_'_(PDB_00674) | ||
| 56 | -GGGCUUGUAGCUCAGGUGGUUAGAGCGCACCCCUGAUAAGGGUGAGGUCGGUGGUUCAAGUCCACUCAGGCCCAC | ||
| 57 | -(((((((..((((.........))))(((((((.....)))))))....(((((.......)))))))))))).. | ||
| 58 | ->>__'CRYSTAL_STRUCTURE_OF_CYSTEINYL-TRNA_SYNTHETASE_BINARY_COMPLEX_WITH_TRNACYS_'_(PDB_00742) | ||
| 59 | -GGCGCGUUAACAAAGCGGUUAUGUAGCGGAUUGCAAAUCCGUCUAGUCCGGUUCGACUCCGGAACGCGCCUCCA | ||
| 60 | -(((((((..(((.........))).((((((.....))))))....(((((.......)))))))))))).... | ||
| 61 | ->>__'CRYSTAL_STRUCTURE_OF_TRNA_NUCLEOTIDYLTRANSFERASE_COMPLEXED_WITH_A_PRIMER_TRNA_AND_AN_INCOMING_ATP_ANALOG_'_(PDB_00767) | ||
| 62 | -GGCCAGGGGCGGUUCGAUUCCGCCCCUGGCCGGCCAGGGGCGGUUCGAUUCCGCCCCUGGCCACCAA | ||
| 63 | -(((((((.(((.........))).)))))))(((((((.(((.........))).)))))))..... | ||
| 64 | ->>__'GLUTAMINYL-TRNA_SYNTHETASE_COMPLEXED_TO_GLUTAMINE_AND_2\'DEOXY_A76_GLUTAMINE_TRNA_'_(PDB_00901) | ||
| 65 | -GGGGUAUCGCCAAGCGGUAAGGCACCGGAUUCUGAUUCCGGCAUUCCGAGGUUCGAAUCCUCGUACCCCAGCCA | ||
| 66 | -((((((..((((.......)))).(((((((...))))))).....(((((.......)))))))))))..... | ||
| 67 | ->>__'IF2,_IF1,_AND_TRNA_FITTED_TO_CRYO-EM_DATA_OF_E._COLI_70S_INITIATION_COMPLEX_'_(PDB_00903) | ||
| 68 | -GCGGAUUUAGCUCAGUUGGGAGAGCGCCAGACUGAAGAUCUGGAGGUCCUGUGUUCGAUCCACAGAAUUCGCACCA | ||
| 69 | -(((((((..((((........))))((((((.......))))))....(((((.......)))))))))))).... | ||
| 70 | ->>__'STRUCTURE_OF_HUMAN_TRYPTOPHANYL-TRNA_SYNTHETASE_IN_COMPLEX_WITH_TRNA(TRP)_'_(PDB_00926) | ||
| 71 | -GACCUCGUGGCGCAAUGGUAGCGCGUCUGACUCCAGAUCAGAAGGUUGCGUGUUCGAAUCACGUCGGGGUCA | ||
| 72 | -((.((((..(((((.....)))))...((((.....)))).......(((((.......))))))))).)). | ||
| 73 | ->>__'CRYSTAL_STRUCTURE_OF_STAPHYLOCOCCUS_AUREUS_TRNA_ADENOSINE_DEAMINASE,_TADA,_IN_COMPLEX_WITH_RNA_'_(PDB_00943) | ||
| 74 | -UUGACUACGGAUCAAUUGACUACGGAUCAAGACUACGGUUUGACUACGGAUCAA | ||
| 75 | -(((((.....)))))(((((.....))))).........(((((.....))))) | ||
| 76 | ->>__'COCRYSTAL_STRUCTURE_OF_AN_RNA_SULFURATION_ENZYME_MNMA_AND_TRNA-GLU_IN_THE_PRE-REACTION_STATE_'_(PDB_00999) | ||
| 77 | -GUCCCCUUCGUCUAGAGGCCCAGGACACCGCCCUUUCACGGCGGUAACAGGGGUUCGAAUCCCCUAGGGG | ||
| 78 | -..((.....(((((.......)))))(((((((.....)))))))....((((.......))))...)). | ||
| 79 | ->>__'STRUCTURE_OF_HUMAN_TRYPTOPHANYL-TRNA_SYNTHETASE_IN_COMPLEX_WITH_TRNA(TRP)_'_(PDB_01002) | ||
| 80 | -GACCUCGUGGCGCAAUGGUAGCGCGUCUGACUCCAGAUCAGAAGGUUGCGUGUUCGAAUCACGUCGGGGUCACCA | ||
| 81 | -(((((((....(((.....)))...((((((.....)))))).....(((((.......)))))))))))).... | ||
| 82 | ->>__'CRYSTAL_STRUCTURE_OF_ARCHAEOGLOBUS_FULGIDUS_O-PHOSPHOSERYL-_TRNA_SYNTHETASE_COMPLEXED_WITH_TRNACYS_AND_O-PHOSPHOSERINE_'_(PDB_01009) | ||
| 83 | -GCCAGGGUGGCAGAGGGGCUUUGCGGCGGACUGCAGAUCCGCUUUACCCCGGUUCGAAUCCGGGCCCUGGC | ||
| 84 | -((((((([[(((]].......)))..((((.......))))......(((((.......)))))))))))) | ||
| 85 | ->>__'CRYSTAL_STRUCTURE_OF_ARCHAEOGLOBUS_FULGIDUS_O-PHOSPHOSERYL-_TRNA_SYNTHETASE_COMPLEXED_WITH_TRNACYS_'_(PDB_01010) | ||
| 86 | -GCCAGGGUGGCAGAGGGGCUUUGCGGCGGACUGCAGAUCCGCUUUACCCCGGUUCGAAUCCGGGCCCUGGC | ||
| 87 | -..((((([[(((]].......)))..(((((.....)))))......(((((.......)))))))))).. | ||
| 88 | ->>__'CRYSTAL_STRUCTURE_OF_ARCHAEOGLOBUS_FULGIDUS_O-PHOSPHOSERYL-_TRNA_SYNTHETASE_E418N/E420N_MUTANT_COMPLEXED_WITH_TRNAOPAL_AND_O-PHOSPHOSERINE_("OPAL_COMPLEX")_'_(PDB_01011) | ||
| 89 | -GCCAGGGUGGCAGAGGGGCUUUGCGGCGGACUUCAGAUCCGCUUUACCCCGGUUCGAAUCCGGGCCCUGGC | ||
| 90 | -(((((((..(((.........))).(((((.......))))).....(((((.......)))))))))))) | ||
| 91 | ->>__'CRYSTAL_STRUCTURE_OF_ARCHAEOGLOBUS_FULGIDUS_O-PHOSPHOSERYL-_TRNA_SYNTHETASE_E418N/E420N_MUTANT_COMPLEXED_WITH_TRNAAMBER_AND_O-PHOSPHOSERINE_("AMBER_COMPLEX")_'_(PDB_01012) | ||
| 92 | -GCCAGGGUGGCAGAGGGGCUUUGCGGCGGACUCUAGAUCCGCUUUACCCCGGUUCGAAUCCGGGCCCUGGC | ||
| 93 | -(((((((..(((.........))).(((((.......))))).....(((((.......)))))))))))) | ||
| 94 | ->>__'CRYSTAL_STRUCTURE_OF_RNASE_Z/TRNA(THR)_COMPLEX_'_(PDB_01053) | ||
| 95 | -GCUUCCAUAGCUCAGCAGGUAGAGCGUCAGCGGUUCGAGCCCGCUUGGAAGCU | ||
| 96 | -(((((((..((((........))))...(((((.......)))))))))))). | ||
| 97 | ->>__'PHENYLALANYL-TRNA_SYNTHETASE_FROM_THERMUS_THERMOPHILUS_COMPLEXED_WITH_TRNA_AND_A_PHENYLALANYL-ADENYLATE_ANALOG_'_(PDB_01134) | ||
| 98 | -GCCGAGGUAGCUCAGUUGGUAGAGCAUGCGACUGAAAAUCGCAGUGUCCGCGGUUCGAUUCCGCGCCUCGGCACCA | ||
| 99 | -(((((((....((........))...((((((.....)))))).....((((.........))))))))))).... | ||
| 100 | ->>__'GLUTAMINYL-TRNA_SYNTHETASE_MUTANT_C229R_WITH_BOUND_ANALOG_5\'-O-[N-(L-GLUTAMINYL)-SULFAMOYL]ADENOSINE_'_(PDB_01258) | ||
| 101 | -GGGGUAUCGCCAAGCGGUAAGGCACCGGAUUCUGAUUCCGGCAUUCCGAGGUUCGAAUCCUCGUACCCCAGCCA | ||
| 102 | -((((((..((((.......)))).(((((((...))))))).....(((((.......)))))))))))..... | ||
| 103 | ->>__'GLUTAMINYL-TRNA_SYNTHETASE_MUTANT_C229R_WITH_BOUND_ANALOG_5\'-O-[N-(L-GLUTAMYL)-SULFAMOYL]ADENOSINE_'_(PDB_01259) | ||
| 104 | -GGGGUAUCGCCAAGCGGUAAGGCACCGGAUUCUGAUUCCGGCAUUCCGAGGUUCGAAUCCUCGUACCCCAGCCA | ||
| 105 | -((((((..((((.......))))((((((((...))))))))....(((((.......)))))))))))..... |
| ... | @@ -312,7 +312,7 @@ def launch_BayesPairing(module_type, seq_, header_, basename): | ... | @@ -312,7 +312,7 @@ def launch_BayesPairing(module_type, seq_, header_, basename): |
| 312 | rna.close() | 312 | rna.close() |
| 313 | 313 | ||
| 314 | def launch_RNAMoIP_worker(x): | 314 | def launch_RNAMoIP_worker(x): |
| 315 | - RNAMoIP = "../RNAMoIP/RNAMoIP.py" | 315 | + RNAMoIP = biorseoDir + "/../RNAMoIP/Src/RNAMoIP.py" |
| 316 | logfile = open("log_of_the_run.sh", 'a') | 316 | logfile = open("log_of_the_run.sh", 'a') |
| 317 | logfile.write(" ".join(["gurobi.sh", RNAMoIP, "-s", '"' +x[1]+'"', "-ss", '"'+x[0].strip()+'"', "-d", descfolder])) | 317 | logfile.write(" ".join(["gurobi.sh", RNAMoIP, "-s", '"' +x[1]+'"', "-ss", '"'+x[0].strip()+'"', "-d", descfolder])) |
| 318 | logfile.write("\n") | 318 | logfile.write("\n") | ... | ... |
-
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