Membrane proteins are central to many cellular processes. From a post-genomic perspective, their importance is demonstrated by the observation that ~25% of genes code for membrane proteins. Thus there are ~8000 membrane proteins encoded within the human genome. Despite the importance of membrane proteins, they remain under-explored territory. High resolution structures are known for ~50 membrane proteins, in contrast to ~22,000 structures for water soluble proteins. Computational methods play an essential role in understanding the relationship between structure and function of membrane proteins. Ion channels, in addition to their intrinsic physiological importance, provide a well studied paradigm for developing such computational approaches for membrane proteins in general. The overall aims of our studies of ion channels are to understand fundamental physical mechanisms of ion channel processes, including permeation, selectivity and gating; and to relate atomic resolution structures of ion channels to their physiological function, with a longer term aim of prediction of the functional consequences of channel mutations. Current research embraces a number of channels, with a particular focus on: (a) potassium channels (voltage gated, Kv, and inward rectifier, Kir, channels); (b) nicotinic acetylcholine receptors and related ‘cys-loop’ receptor-channels; and (c) ionotropic glutamate receptors. Three areas of application of computational methods will be discussed: (a) understanding physical processes of ion and water permeation; (b) development of computational approaches to bridging multiple timescales, enabling us to relate atomic resolution structure to physiological function; and (c) development of accurate models of the mammalian channel proteins based on X-ray structures of bacterial homologues.