Knowledge-based molecular modelling of proteins has proven useful in many instances including the rational design of mutagenesis experiments, but it has been generally limited by the availability of expensive computer hardware and software. To overcome these limitations, we have developed the SWISS-MODEL server for automated knowledge-based protein modelling. The SWISS-MODEL server uses the Brookhaven Protein Data Bank as a source of structural information and automatically generates protein models for sequences which share significant similarities with at least one protein of known 3D-structure. We now use the software framework of the server to generate large collections of protein models. To store these models, we have established the SWISS-MODEL Repository, a new database for protein models generated by theoretical approaches. This repository is directly integrated with SWISS-PROT and other databases through the ExPASy World-Wide Web server.