Progress in genetic engineering has increased the need for, while advances in computational hardware have removed barriers impeding, the development of appropriate computational tools to assist in the understanding of molecular interactions. Advancements both in techniques and in broadening application have been clearly demonstrated. Further development requires progress in the fundamental aspects of theoretical chemistry as well as an increased base of experience in choosing the appropriate set of assumptions for a particular problem. Computer-aided drug design is a current reality, but one that, at its best, supplements an incomplete methodology with the traditional insight and wisdom of an experienced medicinal chemist. In the next few years progress in developing a sound theoretical foundation will make molecular design a realistic aid to the medicinal chemist and protein engineer.