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Ion channels are integral membrane proteins that enable selected ions to flow passively across membranes. Channel proteins have been the focus of computational approaches to relate their three-dimensional (3D) structure to their physiological function. We describe a number of computational tools to model ion channels. Homology modeling may be used to construct structural models of channels based on available X-ray structures. Electrostatics calculations enable an approximate evaluation of the energy profile of an ion passing through a channel. Molecular dynamics simulations and free-energy calculations provide information on the thermodynamics and kinetics of channel function.

Original publication




Journal article


Methods Cell Biol

Publication Date





233 - 265


Computer Simulation, Humans, Ion Channels, Lipid Bilayers, Membrane Proteins, Models, Molecular, Receptors, GABA-A, Sequence Analysis, Protein, Software, Structural Homology, Protein, Thermodynamics