The ability to manipulate ligand-induced conformational change, although representing a major challenge to the protein engineer, is an essential end point in efforts to produce novel functional proteins for biotechnology and therapeutic applications. Progress towards this goal requires determining not only what factors control the fold and stability of a protein, but also how ligand binding alters the complex conformational/energetic landscape. Important strides are being made on several fronts, including understanding the origin of long-range effects and allosteric structural mechanisms, using both experimental and theoretical approaches.