SWISS-MODEL is an automated system for generating 3D protein structure models using homology modeling techniques. The latest version of SWISS-MODEL includes significant improvements and new features, such as the ability to model oligomeric structures and include evolutionary conserved ligands like cofactors or metal ions. The system uses an improved pipeline that heavily relies on model quality estimation to select the most suitable templates, providing estimates of the expected accuracy of the resulting models. The accuracy of SWISS-MODEL is continuously evaluated by the CAMEO system. The new web interface allows users to interactively search for templates, cluster them by sequence similarity, compare alternative templates structurally, and select the best ones for model building. This user-guided template selection step enables the creation of models in different functional states, making SWISS-MODEL a versatile tool for structural modeling in biomedical research.SWISS-MODEL is an automated system for generating 3D protein structure models using homology modeling techniques. The latest version of SWISS-MODEL includes significant improvements and new features, such as the ability to model oligomeric structures and include evolutionary conserved ligands like cofactors or metal ions. The system uses an improved pipeline that heavily relies on model quality estimation to select the most suitable templates, providing estimates of the expected accuracy of the resulting models. The accuracy of SWISS-MODEL is continuously evaluated by the CAMEO system. The new web interface allows users to interactively search for templates, cluster them by sequence similarity, compare alternative templates structurally, and select the best ones for model building. This user-guided template selection step enables the creation of models in different functional states, making SWISS-MODEL a versatile tool for structural modeling in biomedical research.