Advances in X-ray crystallography and protein structure determination have allowed a number of structure-based methods to be developed to facilitate the rapid identification of hit molecules which exert a desired function on a chosen enzyme or protein. Here we present an overview of the structure-based methods that the Fishwick/ Johnson group at the University of Leeds have developed over the last 10 years and present some case studies for which these methods have been successfully applied. These cover antibacterial and anti-infective lead molecule development and hit identification for a range of ion channels and membrane proteins.