Sentence examples for analysis of simulation trajectories from inspiring English sources
According to the analysis of simulation trajectories, the preferred mode of water mediation for conformers is the one donor one acceptor mode.
Finally, analysis of simulation trajectories suggests that the two classes of assembly pathways can be distinguished in single-molecule fluorescence correlation spectroscopy or bulk time-resolved small-angle X-ray scattering experiments.
Step 3: Analysis of simulation trajectory.
The ANGDelMut algorithm is executed in four steps, namely, mutation selection, implicit-solvent molecular dynamics simulation, analysis of simulation trajectory, and data output.
Visualization of simulation trajectories is accomplished using VEGA ZZ [47].
PCA analysis of the simulation trajectories detects and distinguishes two different kinds of motions between the N- and C-terminal subdomains.
A structural analysis of our simulation trajectories revealed not a single, but two distinct association patterns dominated by an interplay between two charged contact points near the binding site.
Based on the conformational and dynamical analysis of the simulation trajectories, we propose that the core coupling elements in the maltose transporter involve contributions from several structural motifs located at the NBD-TMD interface, namely, the EAA loops from the TMDs, and the Q-loop and the ENI motifs from the NBDs.
The GROMOS++ software for the analysis of biomolecular simulation trajectories [14] was used for analyzing the trajectories.
Analysis of the simulation trajectories shows that the foot loop (residues 147 164) undergoes the highest fluctuations within the protein and 6(a)), consistent with the disordered nature of this region in the crystal structure.
To analyze the amount and behavior of the water molecules in the binding pocket and substrate channels, the radial distribution function was calculated using GROMOS++ package for the analysis of biomolecular simulation trajectories.
