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PMC:7441777 / 23585-24886 JSONTXT

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LitCovid-PD-FMA-UBERON

Id Subject Object Predicate Lexical cue fma_id
T38 342-350 Body_part denotes backbone http://purl.org/sig/ont/fma/fma13478
T39 1099-1110 Body_part denotes amino acids http://purl.org/sig/ont/fma/fma82739
T40 1130-1136 Body_part denotes radius http://purl.org/sig/ont/fma/fma23463

LitCovid-PD-MONDO

Id Subject Object Predicate Lexical cue mondo_id
T70 165-173 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091

LitCovid-PD-CLO

Id Subject Object Predicate Lexical cue
T141 93-96 http://purl.obolibrary.org/obo/CLO_0009325 denotes TF1
T142 463-464 http://purl.obolibrary.org/obo/CLO_0001020 denotes A
T143 495-496 http://purl.obolibrary.org/obo/CLO_0001020 denotes A
T144 685-686 http://purl.obolibrary.org/obo/CLO_0001020 denotes Å
T145 693-694 http://purl.obolibrary.org/obo/CLO_0001020 denotes Å
T146 701-702 http://purl.obolibrary.org/obo/CLO_0001020 denotes Å
T147 709-710 http://purl.obolibrary.org/obo/CLO_0001020 denotes Å
T148 717-718 http://purl.obolibrary.org/obo/CLO_0001020 denotes Å
T149 725-726 http://purl.obolibrary.org/obo/CLO_0001020 denotes Å
T150 733-734 http://purl.obolibrary.org/obo/CLO_0001020 denotes Å
T151 741-742 http://purl.obolibrary.org/obo/CLO_0001020 denotes Å
T152 752-753 http://purl.obolibrary.org/obo/CLO_0001020 denotes Å
T153 880-883 http://purl.obolibrary.org/obo/CLO_0009325 denotes TF1
T154 1128-1129 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T155 1142-1143 http://purl.obolibrary.org/obo/CLO_0001020 denotes Å

LitCovid-PD-CHEBI

Id Subject Object Predicate Lexical cue chebi_id
T337 75-85 Chemical denotes remdesivir http://purl.obolibrary.org/obo/CHEBI_145994
T338 87-91 Chemical denotes EGCG http://purl.obolibrary.org/obo/CHEBI_4806
T339 110-113 Chemical denotes TF3 http://purl.obolibrary.org/obo/CHEBI_136608
T340 115-125 Chemical denotes hesperidin http://purl.obolibrary.org/obo/CHEBI_28775
T341 127-136 Chemical denotes myricetin http://purl.obolibrary.org/obo/CHEBI_18152|http://purl.obolibrary.org/obo/CHEBI_58395
T343 142-155 Chemical denotes quercetagetin http://purl.obolibrary.org/obo/CHEBI_8695
T344 351-356 Chemical denotes atoms http://purl.obolibrary.org/obo/CHEBI_33250
T345 763-773 Chemical denotes remdesivir http://purl.obolibrary.org/obo/CHEBI_145994
T346 780-784 Chemical denotes EGCG http://purl.obolibrary.org/obo/CHEBI_4806
T347 791-794 Chemical denotes TF3 http://purl.obolibrary.org/obo/CHEBI_136608
T348 823-832 Chemical denotes myricetin http://purl.obolibrary.org/obo/CHEBI_18152|http://purl.obolibrary.org/obo/CHEBI_58395
T350 839-852 Chemical denotes quercetagetin http://purl.obolibrary.org/obo/CHEBI_8695
T351 859-869 Chemical denotes hesperidin http://purl.obolibrary.org/obo/CHEBI_28775
T352 978-987 Chemical denotes myricetin http://purl.obolibrary.org/obo/CHEBI_18152|http://purl.obolibrary.org/obo/CHEBI_58395
T354 1099-1110 Chemical denotes amino acids http://purl.obolibrary.org/obo/CHEBI_33709
T355 1099-1104 Chemical denotes amino http://purl.obolibrary.org/obo/CHEBI_46882
T356 1105-1110 Chemical denotes acids http://purl.obolibrary.org/obo/CHEBI_37527
T357 1153-1162 Chemical denotes inhibitor http://purl.obolibrary.org/obo/CHEBI_35222

LitCovid-PubTator

Id Subject Object Predicate Lexical cue tao:has_database_id
571 104-108 Gene denotes TF2b Gene:2959
572 176-180 Gene denotes RdRp Gene:43740578
573 758-762 Gene denotes RdRp Gene:43740578
574 775-779 Gene denotes RdRp Gene:43740578
575 786-790 Gene denotes RdRp Gene:43740578
576 796-800 Gene denotes RdRp Gene:43740578
577 801-805 Gene denotes TF2b Gene:2959
578 807-811 Gene denotes RdRp Gene:43740578
579 818-822 Gene denotes RdRp Gene:43740578
580 834-838 Gene denotes RdRp Gene:43740578
581 854-858 Gene denotes RdRp Gene:43740578
582 875-879 Gene denotes RdRp Gene:43740578
583 956-960 Gene denotes RdRp Gene:43740578
584 973-977 Gene denotes RdRp Gene:43740578
585 165-175 Species denotes SARS-CoV-2 Tax:2697049
586 75-85 Chemical denotes remdesivir MESH:C000606551
587 87-91 Chemical denotes EGCG MESH:C045651
588 115-125 Chemical denotes hesperidin MESH:D006569
589 127-136 Chemical denotes myricetin MESH:C040015
590 763-773 Chemical denotes remdesivir MESH:C000606551
591 342-356 Disease denotes backbone atoms

LitCovid-PD-GlycoEpitope

Id Subject Object Predicate Lexical cue glyco_epitope_db_id
T9 93-96 GlycoEpitope denotes TF1 http://www.glycoepitope.jp/epitopes/AN0049
T10 880-883 GlycoEpitope denotes TF1 http://www.glycoepitope.jp/epitopes/AN0049

LitCovid-sentences

Id Subject Object Predicate Lexical cue
T232 0-284 Sentence denotes The 150 ns production simulations carried out for nine systems (complex of remdesivir, EGCG, TF1, TF2a, TF2b, TF3, hesperidin, myricetin, and quercetagetin with the SARS-CoV-2 RdRp) were stable on the basis of the potential energy and total energy (data not shown) of those complexes.
T233 285-466 Sentence denotes Subsequently, the root-mean-square deviations (RMSDs) of backbone atoms relative to their respective initial positions were calculated for each complex and are shown in Figure 3(A).
T234 467-634 Sentence denotes It is evident from Figure 3(A) that all the nine studied systems drifted from their initial positions during the first 50 ns, and after that, they reached equilibrium.
T235 635-918 Sentence denotes The average RMSD values were estimated to be 2.30 Å, 2.45 Å, 1.87 Å, 2.28 Å, 1.68 Å, 2.47 Å, 1.90 Å, 2.03 Å and 1.88 Å for RdRp/remdesivir, RdRp/EGCG, RdRp/TF3, RdRp/TF2b, RdRp/TF2a, RdRp/myricetin, RdRp/quercetagetin, RdRp/hesperidin, and RdRp/TF1 complexes, respectively (Table 3).
T236 919-1020 Sentence denotes The least deviation was observed for RdRp/TF2a, while RdRp/myricetin displayed the highest deviation.
T237 1021-1242 Sentence denotes We also investigated structural variations in the binding site, including all amino acids that fall within a radius of 5 Å from the inhibitor, and the same trend was observed (Figure S2A in the Supplementary Information).
T238 1243-1301 Sentence denotes Overall, this suggests the convergence of our simulations.