Broadly speaking, bottom-up catalyst design is based on detailed understanding of the molecular transformations that govern catalytic processes and controlling these transformations through targeted synthesis of optimal catalysts. In this document, we highlight recent progress in this area and comment on how it might affect the future of catalyst discovery. We mainly focus on the design of optimal active sites for metal alloy catalysts. Rather than focusing on listing relevant examples and success stories, we emphasize the critical framework underpinning these efforts. The central questions we attempt to address are: first, how to identify the critical molecular descriptors of catalytic performance; and second, how to search for optimal active sites based on these critical descriptors.