Abstract Motivation: Information about a particular protein or protein family is usually distributed among multiple databases and often in more than one entry in each database. Retrieval and organization of this information can be a laborious task. This task is complicated even further by the existence of alternative terms for the same concept. Results: The PDB, SWISS-PROT, ENZYME, and CATH databases have been imported into a combined relational database, BioMolQuest. A powerful search engine has been built using this database as a back end. The search engine achieves significant improvements in query performance by automatically utilizing cross-references between the legacy databases. The results of the queries are presented in an organized, hierarchical way. Availability: http://bioinformatics.danforthcenter.org/yury/public/home.html. Unavailable for commercial users. Contact: [email protected] * To whom correspondence should be addressed.