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PMC:7544943 / 13052-15030 JSONTXT

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LitCovid-PD-FMA-UBERON

Id Subject Object Predicate Lexical cue fma_id
T15 1735-1741 Body_part denotes radius http://purl.org/sig/ont/fma/fma23463

LitCovid-PD-MONDO

Id Subject Object Predicate Lexical cue mondo_id
T41 114-122 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T42 138-146 Disease denotes SARS-CoV http://purl.obolibrary.org/obo/MONDO_0005091
T43 1159-1162 Disease denotes PME http://purl.obolibrary.org/obo/MONDO_0020074

LitCovid-PD-CLO

Id Subject Object Predicate Lexical cue
T62 26-28 http://purl.obolibrary.org/obo/CLO_0007622 denotes MD
T63 172-174 http://purl.obolibrary.org/obo/CLO_0007622 denotes MD
T64 527-528 http://purl.obolibrary.org/obo/CLO_0001020 denotes A
T65 726-727 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T66 933-935 http://purl.obolibrary.org/obo/CLO_0008491 denotes ps
T67 1028-1029 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T68 1579-1581 http://purl.obolibrary.org/obo/CLO_0008491 denotes ps

LitCovid-PubTator

Id Subject Object Predicate Lexical cue tao:has_database_id
269 263-267 Gene denotes Mpro Gene:8673700
270 149-153 Gene denotes Mpro Gene:8673700
271 114-124 Species denotes SARS-CoV-2 Tax:2697049
272 138-148 Species denotes SARS-CoV-2 Tax:2697049
273 245-258 Chemical denotes Spro-Piperine
274 575-580 Chemical denotes water MESH:D014867
275 1716-1724 Chemical denotes hydrogen MESH:D006859

LitCovid-sentences

Id Subject Object Predicate Lexical cue
T125 0-4 Sentence denotes 2.4.
T126 6-46 Sentence denotes Molecular dynamics (MD) simulation study
T127 47-322 Sentence denotes To verify the stability of the complex and interaction dynamics of SARS-CoV-2 RBD Spro and SARS-CoV-2 Mpro, we performed the MD simulation study of the two complexes with the highest docking score (Spro-Piperine and Mpro-Piperine), using GROMACS-5.1.5 (Abraham et al., 2015).
T128 323-416 Sentence denotes The CHARMM36 forcefield (Huang & MacKerell, 2013) was used for the simulation of the systems.
T129 417-526 Sentence denotes The topology parameters for the ligand molecule were obtained from CGenFF (Vanommeslaeghe & MacKerell, 2012).
T130 527-623 Sentence denotes A dodecahedron simulation box filled with TIP3P water model (Price & Brooks, 2004) was prepared.
T131 624-700 Sentence denotes Counter ions were added to maintain the electrical neutrality of the system.
T132 701-759 Sentence denotes The systems were kept at a buffer concentration of 0.15 M.
T133 760-861 Sentence denotes Then, the build systems were energy minimized with 50,000 steps using the steepest descent algorithm.
T134 862-1002 Sentence denotes Then the systems were equilibrated under NVT and NPT ensembles for 100 ps at 300 K temperature and 1 atm pressure before the production run.
T135 1003-1095 Sentence denotes After the equilibration, a production run of 100 ns was incorporated under the NPT ensemble.
T136 1096-1258 Sentence denotes For long-range electrostatic interaction, particle mesh Ewald (PME) (Darden et al., 1993) and for van der Waals interactions, the force-switching scheme was used.
T137 1259-1489 Sentence denotes Besides, for temperature and pressure coupling, the Berendsen thermostat (Berendsen et al., 1984) with velocity rescaling and Parrinello-Rahman barostat (Parrinello & Rahman, 1981) with isotropic rescaling were used, respectively.
T138 1490-1582 Sentence denotes The simulation time step was set to 2 fs, and the trajectories were recorded at every 10 ps.
T139 1583-1788 Sentence denotes The simulation data were analysed by analysing the root mean square deviation (RMSD), root mean square fluctuation (RMSF), number of hydrogen bonds and radius of gyration (Rg) using Gromacs analysis tools.
T140 1789-1898 Sentence denotes The principal component analysis (PCA) was performed using the g_covar, g_anaeig and g_sham tools of Gromacs.
T141 1899-1978 Sentence denotes The data were exported to origin 9.0 and plotted for further analysis purposes.

2_test

Id Subject Object Predicate Lexical cue
32938313-23832629-56197381 367-371 23832629 denotes 2013
32938313-23146088-56197382 520-524 23146088 denotes 2012
32938313-15549884-56197383 604-608 15549884 denotes 2004