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LitCovid-PubTator

Id Subject Object Predicate Lexical cue tao:has_database_id
209 96-101 Gene denotes spike Gene:43740568
210 650-655 Gene denotes spike Gene:43740568
211 1253-1258 Gene denotes spike Gene:43740568
212 740-758 Gene denotes –6, –4, –6, and –4
213 85-95 Species denotes SARS-CoV-2 Tax:2697049
214 349-354 Chemical denotes water MESH:D014867
215 593-598 Chemical denotes water MESH:D014867
216 851-856 Chemical denotes water MESH:D014867
217 1310-1315 Chemical denotes rutin MESH:D012431
221 2014-2015 Gene denotes τ Gene:4137
222 2056-2057 Gene denotes τ Gene:4137
223 2271-2279 Chemical denotes hydrogen MESH:D006859
226 3871-3876 Gene denotes spike Gene:43740568
227 3673-3681 Chemical denotes hydrogen MESH:D006859
230 4166-4171 Gene denotes spike Gene:43740568
231 4834-4837 Disease denotes VMD

LitCovid-sentences

Id Subject Object Predicate Lexical cue
T87 0-4 Sentence denotes 2.4.
T88 6-80 Sentence denotes Molecular dynamics trajectory analysis of protein and their docked complex
T89 81-242 Sentence denotes The SARS-CoV-2 spike protein and main protease were used separately for molecular dynamics (MD) simulations alone and in complex with the repurposed drug, rutin.
T90 243-456 Sentence denotes All the four MD simulations were executed through GROMACS v5.0 under the force field GROMOS96 54a7 having water model SPC216 along with the time step of 1 fs for 100 ns (Abraham et al., 2015; Darden et al., 1993).
T91 457-629 Sentence denotes Varied sizes of the simulation box were created for each MD simulation event, which were further loaded with about respective amount of water molecules using the SPC model.
T92 630-920 Sentence denotes The total charge on spike protein, main protease and the two in complex with rutin were neutralized by adding –6, –4, –6, and –4 charges, respectively, and were incorporated into the simulation system by compensating the water molecules in the arbitrary locations inside the simulation box.
T93 921-1023 Sentence denotes The NPT ensembles, along with periodic boundary conditions, were utilized to carry out MD simulations.
T94 1024-1100 Sentence denotes A cut-off of about 12 Å was used in order to manage the Vander Waals forces.
T95 1101-1248 Sentence denotes The Particle Mesh Ewald model manifesting a cut-off of 14 Å was further utilized to calculate the electrostatic interactions (Darden et al., 1993).
T96 1249-1378 Sentence denotes The spike protein, main protease and the two in complex with rutin were solvated through a slab of about 10 Å in every direction.
T97 1379-1433 Sentence denotes The neighbor list was updated to a frequency of 10 ps.
T98 1434-1514 Sentence denotes The MD simulations were achieved for each system employing the four major steps.
T99 1515-1704 Sentence denotes The first step deals with the energy minimization of the entire system utilizing the integrator of steepest descent in continuation with second integrator of conjugate gradients algorithms.
T100 1705-1935 Sentence denotes The second step involves the minimization and molecular dynamics of NVT and NPT ensembles for 500 ps and 1000 ps, respectively allowing the solvents and ions to evolve by keeping the same starting configuration for the structures.
T101 1936-2137 Sentence denotes In the third step the systems were heated using a lower temperature coupling (τ = 0.1 ps) along with pressure coupling (τ = 0.5 ps) to attain equilibrium at 300 K and 1 atm of temperature and pressure.
T102 2138-2266 Sentence denotes In the equilibration phase, the thermostat and barostat were evaluated through the Berendsen algorithm (Berendsen et al., 1984).
T103 2267-2378 Sentence denotes The hydrogen-containing bond lengths were constrained with the help of the LINCS algorithm (Hess et al., 1997).
T104 2379-2610 Sentence denotes Finally, the last step also called as the production step was carried out, where the MD simulation for 100 ns at 300 K temperature with 2 fs of time step were performed for both systems, and the last final structures were achieved.
T105 2611-2709 Sentence denotes The Maxwell Boltzmann distribution was utilized in order to reassign the velocities at every step.
T106 2710-2872 Sentence denotes The Nose Hoover thermostat and Parrinello Rahman barostat were the respective thermostat and barostat for the final MD or production run (Berendsen et al., 1984).
T107 2873-2959 Sentence denotes Various analyses were performed with the help of inbuilt analysis commands of GROMACS.
T108 2960-3203 Sentence denotes The root mean square deviation (RMSD) is a magnitude of the dimensional disparity among the two stagnant structures, and RMSD calculation is achieved depending upon the native structure and each consecutive trajectory frames in the simulation.
T109 3204-3412 Sentence denotes In addition, root mean square fluctuation (RMSF) profile measures the affability of every protein residue depending on the fluctuation about an average location within all MD simulations (Knapp et al., 2011).
T110 3413-3531 Sentence denotes Therefore, RMSD and RMSF of each simulation system were determined to examine the stability and residual fluctuations.
T111 3532-3662 Sentence denotes Further, the radius of gyration (Rg) analysis was performed to evaluate the compactness of both the simulation systems separately.
T112 3663-3952 Sentence denotes Also, the hydrogen bond analysis was performed to check the neighboring interactions with both simulation systems separately, including the hydrophobic interactions with the help of the LigPlot tool for both spike protein and main protease complexes with rutin before and after simulation.
T113 3953-4098 Sentence denotes Additionally, the solvent accessibility surface area (SASA) was also computed to examine the solvent attributable areas of all simulation system.
T114 4099-4345 Sentence denotes The cluster analysis having a cut-off value of 0.25 and 0.2 nm for spike protein and main protease respectively, depending upon the RMSD profile were utilized to demonstrate the conformations found utmost intermittently throughout the trajectory.
T115 4346-4483 Sentence denotes Here, all the structures having RMSD values of below 0.25 nm for all components within a cluster are incorporated to the initial cluster.
T116 4484-4617 Sentence denotes It is rare that a molecule having a higher value for RMSD than 0.25 nm from other cluster supposedly would be treated as a structure.
T117 4618-4715 Sentence denotes The secondary structure analysis was also performed using the DSSP program (Martin et al., 2005).
T118 4716-4905 Sentence denotes The visualization of protein nature during the entire simulation was accomplished by using Visual Molecular Dynamics (VMD) (Humphrey et al., 1996) and UCSF Chimera (Pettersen et al., 2004).