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Molecular dynamics (MD) simulations have become a powerful and popular method for the study of protein allostery, the widespread phenomenon in which a stimulus at one site on a protein influences the properties of another site on the protein. By capturing the motions of a protein's constituent atoms, simulations can enable the discovery of allosteric binding sites and the determination of the mechanistic basis for allostery. These results can provide a foundation for applications includingdoi:10.1371/journal.pcbi.1004746 pmid:27285999 pmcid:PMC4902200 fatcat:olv67vwnirgvlgm6e7uplgeejm