CDD Vault introduces zero-click automated QSAR modeling, a fully hands-off AutoML system that continuously trains, evaluates, and deploys models using large-scale benchmarking and rigorous cross-validation. Users can also run deep-learning similarity searches, identify novel bioisosteres, and perform 3D protein folding and ligand–protein docking with AlphaFold2, ESMFold, DiffDock, and Boltz2, generating scores, poses, and interactive visualizations. These AI tools integrate directly into registration, search, and analysis workflows to transform multidisciplinary data into actionable insights. CDD Vault unifies chemically aware data management capturing structures, sequences, conjugation details, and assay results accelerating modern drug discovery and collaboration.