Adam Hospital,1 Josep Ramon Goñi,2,3 Modesto Orozco,1–4 Josep L Gelpí2–4 1Institute for Research in Biomedicine, The Barcelona Institute of Science and Technology, 2Joint BSC-IRB Research Program in Computational Biology, 3Barcelona Supercomputing Center, 4Department of Biochemistry and Molecular Biology, University of Barcelona, Barcelona, Spain 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