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Molecular Dynamics Simulations in Drug Design

Definition

Molecular dynamics (MD) is a computational tool to simulate the motions of a molecular system. The method requires an interaction potential from which interatomic forces can be calculated and equations of motion that govern the dynamics of the system. MD simulations sample the configuration space and generate a trajectory that follows molecular movements as a function of time. Originally developed to study properties of the liquid state, MD simulations are nowadays routinely applied to macromolecular systems of biological and pharmaceutical interest. Applications include the refinement of experimentally determined structures, conformational analysis and protein homology modeling, the elucidation of biochemical and biophysical mechanisms at the atomic level, docking of biomolecular complexes and a variety of approaches for calculating free energy changes. Most of these tasks are of utmost importance in structure-based drug design.