Neo4j, a graph database, enables data scientists and chemists to analyze molecules for drug development by faithfully mirroring real-world structures at the molecular level. By modeling molecules as graphs, researchers can explore interactions between atoms and bonds, and identify properties such as solubility. This approach allows for the identification of surprising results, such as the importance of certain fragments in a molecule's permeability across membranes. To get started with graph databases like Neo4j, it is recommended to carefully design a schema, start with small datasets, and iterate until finding a scalable solution.