Structural analyses of drugs and pesticides can enable the identification of new bioactive compounds with novel and diverse scaffolds as well as improve our understanding of the bioactive fragment space. The Pesticide And Drug Fragments (PADFrag) database is a unique bioinformatic-cheminformatic cross-referencing resource that combines detailed bioactive fragment data and potential targets with a strong focus on quantitative, analytic, and molecular-scale information for the exploration of bioactive fragment space for drug discovery ( http://chemyang.ccnu.edu.cn/ccb/database/PADFrag/ ). The main applications of PADFrag are the analysis of the privileged structures within known bioactive molecules, ab initio molecule library design, and core fragment discovery for fragment-based drug design. Other potential applications include prediction of fragment interactions and general pharmaceutical research.