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Molecular dynamics simulations: advances and applications

2015; Dove Medical Press; Linguagem: Inglês

10.2147/aabc.s70333

1178-6949

Josep Lluis Gelpí, Adam Hospital, Ramón Goñi, Modesto Orozco,

Computational Drug Discovery Methods

Abstract: Molecular dynamics simulations have evolved into a mature technique that can be used effectively to understand macromolecular structure-to-function relationships. Present simulation times are close to biologically relevant ones. Information gathered about the dynamic properties of macromolecules is rich enough to shift the usual paradigm of structural bioinformatics from studying single structures to analyze conformational ensembles. Here, we describe the foundations of molecular dynamics and the improvements made in the direction of getting such ensemble. Specific application of the technique to three main issues (allosteric regulation, docking, and structure refinement) is discussed. Keywords: molecular dynamics, allostery, docking, conformational ensembles, structure prediction, refinement