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Chapter 12 Molecular Modeling and Simulation Studies of Ion Channel Structures, Dynamics and Mechanisms

Elsevier Science & Technology
DOI: 10.1016/s0091-679x(08)00812-1
  • Biology
  • Computer Science
  • Physics


Abstract 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.

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