LitCovid-sentences  

PMC:7544943 / 13099-15030 JSONTXT 7 Projects

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Id Subject Object Predicate Lexical cue
T127 0-275 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 276-369 Sentence denotes The CHARMM36 forcefield (Huang & MacKerell, 2013) was used for the simulation of the systems.
T129 370-479 Sentence denotes The topology parameters for the ligand molecule were obtained from CGenFF (Vanommeslaeghe & MacKerell, 2012).
T130 480-576 Sentence denotes A dodecahedron simulation box filled with TIP3P water model (Price & Brooks, 2004) was prepared.
T131 577-653 Sentence denotes Counter ions were added to maintain the electrical neutrality of the system.
T132 654-712 Sentence denotes The systems were kept at a buffer concentration of 0.15 M.
T133 713-814 Sentence denotes Then, the build systems were energy minimized with 50,000 steps using the steepest descent algorithm.
T134 815-955 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 956-1048 Sentence denotes After the equilibration, a production run of 100 ns was incorporated under the NPT ensemble.
T136 1049-1211 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 1212-1442 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 1443-1535 Sentence denotes The simulation time step was set to 2 fs, and the trajectories were recorded at every 10 ps.
T139 1536-1741 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 1742-1851 Sentence denotes The principal component analysis (PCA) was performed using the g_covar, g_anaeig and g_sham tools of Gromacs.
T141 1852-1931 Sentence denotes The data were exported to origin 9.0 and plotted for further analysis purposes.