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1 additions
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106 deletions
data/sec_structs/verified_tRNAs.dbn
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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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