Despite the increasing number of recently solved membrane protein strictures, coverage of membrane protein fold space remains relatively sparse. This necessitates the use of computational strategies to investigate membrane protein structure, allowing us to further our understanding of how membrane proteins carry out their diverse range of functions, while aiding the development of novel predictive tools with which to probe uncharacterised folds. Analysis of known structures, the application of machine learning techniques, molecular dynamics simulations and protein structure prediction have enabled significant advances to be made in the field of membrane protein research. In this communication, the key bioinformatic methods that allow the characterisation of membrane proteins are reviewed, the tools available for the structural analysis of membrane proteins are presented and the contribution these tools have made to expanding our understanding of membrane protein structure, function and stability is discussed. (C) 2011 Elsevier Inc. All rights reserved.