Recent advances in experimental techniques have led to an enormous explosion of available data about protein–ligand complexes. To exploit the information that is hidden in these large data, collection tools for managing and accessing huge data collections are needed. This paper discusses databases for protein–ligand data which are accessible via the World Wide Web. A strong focus is placed on the ReLiBase database system which is a new three-dimensional database for storing and analysing structures of protein–ligand complexes currently deposited in the Brookhaven Protein Data Bank (PDB). ReLiBase contains efficient query tools for identifying and analysing ligands and protein–ligand complexes. Its application for structure-based drug design is illustrated.