Advances in the field of drug discovery have brought an explosion in the quantity of data available to medicinal chemists and other project team members. New strategies and systems are needed to help these scientists to efficiently gather, organize, analyze, annotate, and share data about potential new drug molecules of interest to their project teams. Herein we describe a suite of integrated services and end-user applications that facilitate these activities throughout the medicinal chemistry design cycle. The Automated Data Presentation (ADP) and Virtual Compound Profiler (VCP) processes automate the gathering, organization, and storage of real and virtual molecules, respectively, and associated data. The Project-Focused Activity and Knowledge Tracker (PFAKT) provides a unified data analysis and collaboration environment, enhancing decision-making, improving team communication, and increasing efficiency.