LitCovid-sentences  

PMC:7441777 / 13861-16786 JSONTXT 7 Projects

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Id Subject Object Predicate Lexical cue
T149 0-4 Sentence denotes 2.2.
T150 6-36 Sentence denotes Molecular dynamics simulations
T151 37-313 Sentence denotes All-atom molecular dynamics (MD) simulations were performed on the best eight selected plant-derived natural polyphenols obtained from the molecular docking study along with remdesivir, a well-known RdRp inhibitor, for studying thermodynamic stability of the docked structure.
T152 314-359 Sentence denotes The pmemd.cuda module in AMBER18 (Case et al.
T153 360-481 Sentence denotes 2018) was used for conducting MD simulations, and all simulations were performed utilizing the graphics card, RTX 2080Ti.
T154 482-625 Sentence denotes We adopted the same protocol that was used in our earlier studies (Jonniya et al., 2019; Sk, Roy, Jonniya, et al., 2020; Sk, Roy, & Kar, 2020).
T155 626-771 Sentence denotes The receptor and small molecules were described by the Amber ff14SB (Maier et al., 2015) and GAFF2 (Wang et al., 2004) force field, respectively.
T156 772-905 Sentence denotes Ligands were assigned the AM1-BCC (Jakalian et al., 2002) atomic charges calculated using the antechamber (Wang et al., 2001) module.
T157 906-1071 Sentence denotes The complexes were then solvated using an explicit TIP3P (Price & Brooks III, 2004) water model, and nearly 38124 water molecules were needed to solvate each system.
T158 1072-1167 Sentence denotes Subsequently, all solvated systems were neutralized by adding an appropriate number of Na+ ion.
T159 1168-1276 Sentence denotes All bond lengths, including hydrogen atoms, were constrained by the SHAKE algorithm (Kräutler et al., 2001).
T160 1277-1319 Sentence denotes This allows the usage of a 2 fs time-step.
T161 1320-1484 Sentence denotes The non-bonded cut-off was set to 8 Å and the long range electrostatic interactions were evaluated using the particle-mesh Ewald (PME) (Darden et al., 1993) method.
T162 1485-1612 Sentence denotes The temperature was kept at 300 K using the Langevin thermostat (Loncharich et al., 1992) with a collision frequency of 2 ps−1.
T163 1613-1718 Sentence denotes The system pressure was controlled by Berendsen’s Barostat (Berendsen et al., 1984) and fixed at 1.0 bar.
T164 1719-1769 Sentence denotes We used a time-step of 2.0 fs for all simulations.
T165 1770-1814 Sentence denotes Briefly, we used two stages of minimization.
T166 1815-2089 Sentence denotes Firstly, each complex was optimized by 500 steps of steepest descent followed by another 500 steps of conjugate gradient minimization, keeping all atoms of the complex restrained to their initial coordinate with a weak harmonic potential (force constant 2.0 kcal mol−1 Å−2).
T167 2090-2310 Sentence denotes The second stage of minimization was carried out without any restraints by performing 100 steps of steepest descent, followed by another 900 steps of conjugate gradient minimization to remove any residual steric clashes.
T168 2311-2467 Sentence denotes Subsequently, all systems were gradually heated from 0 K to 300 K at the NVT ensemble with a force constant of 2.0 kcal mol−1Å−2 acting on all solute atoms.
T169 2468-2542 Sentence denotes Next, 1.0 ns equilibration MD phase was carried out without any restraint.
T170 2543-2636 Sentence denotes Finally, we performed 150 ns production simulations for all four systems at the NPT ensemble.
T171 2637-2818 Sentence denotes Overall, we accumulated 15000 conformations for each simulation, and we used 500 snapshots from the last 50 ns trajectories for binding affinity estimation using the MM-PBSA scheme.
T172 2819-2925 Sentence denotes The trajectory analysis was done by the AmberTools19 CPPTRAJ (Roe & Cheatham III, 2013) module of Amber18.