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PMC:7544934 / 20175-21614 JSONTXT

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LitCovid-PubTator

Id Subject Object Predicate Lexical cue tao:has_database_id
472 34-38 Gene denotes ACE2 Gene:59272
473 317-321 Gene denotes ACE2 Gene:59272
474 984-988 Gene denotes ACE2 Gene:59272
475 1109-1113 Gene denotes ACE2 Gene:59272
476 989-999 Chemical denotes Naltrexone MESH:D009271
477 89-97 Disease denotes atoms MD MESH:D009436

LitCovid-sentences

Id Subject Object Predicate Lexical cue
T149 0-131 Sentence denotes The dynamics stability of the RBD-ACE2-naltrexone complex was analyzed by performing all-atoms MD simulations of 100 ns in GROMACS.
T150 132-296 Sentence denotes The backbone RMSD analysis provides important information on the stability of protein and protein-ligand complexes and the time when simulation reached equilibrium.
T151 297-422 Sentence denotes The RMSD of the RBD-ACE2-naltrexone complex displayed an average RMSD ∼2.46 Å throughout the entire simulation (Figure 3(A)).
T152 423-574 Sentence denotes Besides, the RMSD of ligand was also found to be stable (red line in Figure 3(A)) with very minimal deviation as compared to the starting conformation.
T153 575-736 Sentence denotes Overall, the complex system displayed the least backbone deviation, indicates that docked conformation is accurate and remained stable over the 100 ns timescale.
T154 737-939 Sentence denotes Radiuses of gyration assess the compactness of the system, where a compact gyradius of ∼3.24 nm for the complex indicates the consistent shape and size of the system during the simulation (Figure 3(B)).
T155 940-1088 Sentence denotes The residue flexibility of protease and RBD-ACE2/Naltrexone complex was examined by performing Cα RMSF analysis of both the sub-units (Figure 3(C)).
T156 1089-1229 Sentence denotes The average RMSF of ACE2 was found to be 0.14 nm, while for the RBD it was reported to be 0.17 nm (for the receptor-binding motif ∼0.16 nm).
T157 1230-1439 Sentence denotes The receptor-binding motif of RBD displayed a high degree of flexibility and the residues participated in the ligand interaction also portrayed higher RMSF indicating their participation in ligand recognition.