title: Molecular modeling and simulation studies of ion channel structures, dynamics and mechanisms.
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.
authors.affiliation: Department of Biochemistry, University of Oxford, Oxford, United Kingdom.
authors.forename: Kaihsu
authors.initials: K
authors.lastname: Tai
authors.forename: Philip
authors.initials: P
authors.lastname: Fowler
authors.forename: Younes
authors.initials: Y
authors.lastname: Mokrab
authors.forename: Phillip
authors.initials: P
authors.lastname: Stansfeld
authors.forename: Mark S P
authors.initials: MS
authors.lastname: Sansom
mesh_terms: D003198:Computer Simulation; D006801:Humans; D007473:Ion Channels / Q000737:chemistry* / Q000378:metabolism*; D008051:Lipid Bilayers / Q000378:metabolism; D008565:Membrane Proteins / Q000737:chemistry / Q000378:metabolism; D008958:Models, Molecular; D011963:Receptors, GABA-A / Q000737:chemistry; D020539:Sequence Analysis, Protein; D012984:Software; D040681:Structural Homology, Protein; D013816:Thermodynamics
chemical_list: D007473:Ion Channels; D008051:Lipid Bilayers; D008565:Membrane Proteins; D011963:Receptors, GABA-A