The SWISS-MODEL Repository is a comprehensive database of 3D protein structure models generated by the SWISS-MODEL homology-modelling pipeline. It aims to provide access to an up-to-date collection of annotated 3D protein models for all sequences in the Swiss-Prot database and relevant model organisms. As of September 2008, the repository contains 3.4 million entries for 2.7 million different protein sequences from the UniProt database. The repository allows users to assess model quality, search for alternative template structures, and build models interactively via the SWISS-MODEL Workspace. It also integrates with other databases such as the Protein Model Portal to facilitate navigation between protein sequence and structure resources. The repository's content, access, and interface are detailed, including the homology modelling process, model database structure, and web-based services. Future directions include updates to reflect the growth of sequence and structure databases, and the inclusion of models for oligomeric assemblies and proteins with essential cofactors.The SWISS-MODEL Repository is a comprehensive database of 3D protein structure models generated by the SWISS-MODEL homology-modelling pipeline. It aims to provide access to an up-to-date collection of annotated 3D protein models for all sequences in the Swiss-Prot database and relevant model organisms. As of September 2008, the repository contains 3.4 million entries for 2.7 million different protein sequences from the UniProt database. The repository allows users to assess model quality, search for alternative template structures, and build models interactively via the SWISS-MODEL Workspace. It also integrates with other databases such as the Protein Model Portal to facilitate navigation between protein sequence and structure resources. The repository's content, access, and interface are detailed, including the homology modelling process, model database structure, and web-based services. Future directions include updates to reflect the growth of sequence and structure databases, and the inclusion of models for oligomeric assemblies and proteins with essential cofactors.