Then the system is energy minimized and equilibrated by solving Newton's equations of motion until the properties of the system no longer change with time.
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After equilibration, a production run is performed for an appropriate period of time to output trajectories, which are then analyzed for the properties of interest. Specifically, simulation can be performed to characterize protein flexibility, refine experimentally determined structures, evaluate protein-ligand binding, study biocatalysis or even monitor the protein folding process.
MD simulation is also particularly useful in computer-aided drug discovery for the identification of cryptic or allosteric binding sites, the enhancement of traditional virtual-screening methodologies, and the direct prediction of small-molecule binding energies. Please do not hesitate to contact us for more details about our molecular dynamics simulation service.
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