Sentence examples for molecular simulation trajectories from inspiring English sources

Using this tool, Molmil can e.g. be used to produce high quality MP4 videos of molecular simulation trajectories.

Furthermore, Molmil can also be used to easily load files from the users' hard drive, including molecular simulation trajectories, and comes with a readily accessible command line interface, which is also programmable by embedding the commands in the URL, as shown in e.g. Fig. 2.

MSMs provide a summarized view of the ensemble of spontaneous fluctuations exhibited by the protein at equilibrium by stitching together a set of individual short molecular simulation trajectories.

One- and two-stage free energy methods are common approaches for calculating the chemical potential from a molecular dynamics or Monte Carlo molecular simulation trajectory.

For neuraminidase and cyclin-dependent kinase II, snapshots of molecular dynamics simulation trajectories have been clustered and structurally assessed by applying a variety of methods.

To confirm the conformational transitions for Escherichia coli ADK, we also measured the domain motion of ADK using the geometric center distances of NMP and LID domains with CORE domain along the molecular dynamics simulation trajectories.

The findings result from an analysis of unbiased atomistic molecular dynamics simulation trajectories (totaling >14 μs) of the hDAT molecule immersed in lipid membrane environments with or without phosphatidylinositol 4,5-biphosphate (PIP2) lipids.

To check whether our simulations involved the large-scale conformational transitions of ADK, we calculated the RMS deviations of the C α atoms from both open (4ake.pdb) and closed (1ake.pdb) conformations of ADK along all the molecular dynamics simulation trajectories.

One possibility, which we call a fully-flexible receptor model, is to use a molecular dynamics simulation trajectory of the receptor to simulate its explicit flexibility.

In this study, we developed three ideas: utilizing the structural ensemble sampled from a molecular dynamics simulation trajectory, using multiple peptide templates, and optimizing the sequence-structure mapping.

In this study, we propose three ideas for improving our ability to predict the binding energy between SH3 domains and peptides: (1) utilizing the structural ensembles sampled from a molecular dynamics simulation trajectory, (2) utilizing multiple peptide templates, and (3) optimizing the sequence-structure mapping.