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PMC:7102553 / 7883-9142 JSONTXT

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LitCovid-PubTator

Id Subject Object Predicate Lexical cue tao:has_database_id
226 134-139 Gene denotes GRP78 Gene:3309
227 226-231 Gene denotes GRP78 Gene:3309
228 584-589 Gene denotes GRP78 Gene:3309
229 660-665 Gene denotes GRP78 Gene:3309
230 463-470 Species denotes HADDOCK Tax:8056
231 995-1002 Species denotes HADDOCK Tax:8056
232 1237-1244 Species denotes HADDOCK Tax:8056
233 241-244 Chemical denotes ATP MESH:D000255
234 405-410 Chemical denotes water MESH:D014867
235 87-95 Disease denotes COVID-19 MESH:C000657245
236 543-551 Disease denotes COVID-19 MESH:C000657245
237 808-816 Disease denotes COVID-19 MESH:C000657245

LitCovid-PD-FMA-UBERON

Id Subject Object Predicate Lexical cue fma_id
T57 823-830 Body_part denotes protein http://purl.org/sig/ont/fma/fma67257
T58 912-920 Body_part denotes proteins http://purl.org/sig/ont/fma/fma67257
T59 1028-1038 Body_part denotes amino acid http://purl.org/sig/ont/fma/fma82739
T60 1073-1081 Body_part denotes proteins http://purl.org/sig/ont/fma/fma67257
T61 1149-1156 Body_part denotes protein http://purl.org/sig/ont/fma/fma67257

LitCovid-PD-MONDO

Id Subject Object Predicate Lexical cue mondo_id
T40 87-95 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T41 543-551 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096
T42 808-816 Disease denotes COVID-19 http://purl.obolibrary.org/obo/MONDO_0100096

LitCovid-PD-CLO

Id Subject Object Predicate Lexical cue
T73 34-38 http://purl.obolibrary.org/obo/UBERON_0000473 denotes test
T74 666-672 http://purl.obolibrary.org/obo/CLO_0001658 denotes active
T75 783-789 http://purl.obolibrary.org/obo/CLO_0001658 denotes active
T76 912-934 http://purl.obolibrary.org/obo/CHEBI_33708 denotes proteins, the residues
T77 951-957 http://purl.obolibrary.org/obo/CLO_0001658 denotes active
T78 1004-1010 http://purl.obolibrary.org/obo/CLO_0001658 denotes Active
T79 1028-1047 http://purl.obolibrary.org/obo/CHEBI_33708 denotes amino acid residues
T80 1028-1047 http://purl.obolibrary.org/obo/PR_000036907 denotes amino acid residues
T81 1249-1251 http://purl.obolibrary.org/obo/CLO_0001302 denotes 34
T82 1253-1255 http://purl.obolibrary.org/obo/CLO_0001000 denotes 35
T83 1257-1259 http://purl.obolibrary.org/obo/CLO_0001313 denotes 36

LitCovid-PD-CHEBI

Id Subject Object Predicate Lexical cue chebi_id
T48 241-244 Chemical denotes ATP http://purl.obolibrary.org/obo/CHEBI_15422|http://purl.obolibrary.org/obo/CHEBI_30616
T50 405-410 Chemical denotes water http://purl.obolibrary.org/obo/CHEBI_15377
T51 411-415 Chemical denotes ions http://purl.obolibrary.org/obo/CHEBI_24870
T52 424-430 Chemical denotes ligand http://purl.obolibrary.org/obo/CHEBI_52214
T53 823-830 Chemical denotes protein http://purl.obolibrary.org/obo/CHEBI_36080
T54 912-920 Chemical denotes proteins http://purl.obolibrary.org/obo/CHEBI_36080
T55 1028-1038 Chemical denotes amino acid http://purl.obolibrary.org/obo/CHEBI_33709
T56 1028-1033 Chemical denotes amino http://purl.obolibrary.org/obo/CHEBI_46882
T57 1034-1038 Chemical denotes acid http://purl.obolibrary.org/obo/CHEBI_37527
T58 1073-1081 Chemical denotes proteins http://purl.obolibrary.org/obo/CHEBI_36080
T59 1149-1156 Chemical denotes protein http://purl.obolibrary.org/obo/CHEBI_36080

LitCovid-sentences

Id Subject Object Predicate Lexical cue
T44 0-173 Sentence denotes Molecular docking was utilized to test the binding affinity of the four regions of the COVID-19 spike against the solved structure of GRP78 Substrate Binding Domain (SBD) β.
T45 174-431 Sentence denotes The only solved structure of wild-type, full-length GRP78 bound to ATP in the open configuration found in the PDB database is 5E84.30 , 31 The coordinates of 5E84 were downloaded and prepared for the docking experiment by removing water ions and the ligand.
T46 432-903 Sentence denotes The solvated docking software, HADDOCK, was used in this study to dock the four regions of the spike model for COVID-19 against the solved structure of GRP78.32 The easy interface was utilized since no restraints are defined.33 GRP78 active residues (I426, T428, V429, V432, T434, F451, S452, V457, and I459) were retrieved from the literature.30 The active residues from the COVID-19 spike protein were chosen for each region of the spike to be the hydrophobic residues.
T47 904-1003 Sentence denotes In both proteins, the residues surrounding the active residues were selected as passive in HADDOCK.
T48 1004-1259 Sentence denotes Active residues are the amino acid residues from the two interacting proteins’ binding sites that take part in direct interaction with the other protein partner while passive residues are the residues that can interact indirectly in HADDOCK.33, 34, 35, 36

2_test

Id Subject Object Predicate Lexical cue
32169481-26655470-61108489 305-307 26655470 denotes 30
32169481-29084938-61108490 310-312 29084938 denotes 31
32169481-16899489-61108491 590-592 16899489 denotes 32
32169481-20431534-61108492 657-659 20431534 denotes 33
32169481-26655470-61108493 776-778 26655470 denotes 30
32169481-20431534-61108494 1245-1247 20431534 denotes 33
32169481-17803234-61108495 1249-1251 17803234 denotes 34
32169481-15981252-61108496 1253-1255 15981252 denotes 35
32169481-12580598-2046607 1257-1259 12580598 denotes 36