Abstract
Molecular dynamics (MD) simulation is an emerging in silico technique with potential applications in diverse areas of pharmacology. Over the past three decades MD has evolved as an area of importance for understanding the atomic basis of complex phenomena such as molecular recognition, protein folding, and the transport of ions and small molecules across membranes. The application of MD simulations in isolation and in conjunction with experimental approaches have provided an increased understanding of protein structure-function relationships and demonstrated promise in drug discovery.
Highlights
Perspective Molecular Dynamics (MD) simulations are computational approaches based on Newton’s equations of motion and statistical mechanics principles that relate the motions and distributions of atoms and molecules
In MD simulations the forces between atoms and the potential energy of the system are defined by molecular mechanics biomolecular force fields
The importance of simulation techniques arises from the fact that biomacromolecules such as proteins exist in a dynamic state of motion
Summary
Perspective Molecular Dynamics (MD) simulations are computational approaches based on Newton’s equations of motion and statistical mechanics principles that relate the motions and distributions of atoms and molecules. In MD simulations the forces between atoms and the potential energy of the system are defined by molecular mechanics biomolecular force fields. To understand more complex biomolecular events such as large domain motions, protein folding, protein-ligand binding and the transport of molecules across membranes, simulation timescales of microseconds to milliseconds are required (Dror et al 2012).
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