SWISS-MODEL: modelling protein tertiary and quaternary structure using evolutionary information

SWISS-MODEL is a fully automated protein structure homology-modelling server with a user-friendly web interface, used to generate 3D models for proteins that lack experimental structures. This paper describes its latest version, whose template library annotates quaternary structure plus essential ligands and cofactors so that complete structural models, including oligomeric assemblies, can be built. The improved pipeline relies heavily on model quality estimation to select the most suitable templates and to provide estimates of expected model accuracy.

The accuracy of SWISS-MODEL models is continuously evaluated by the CAMEO system, and the redesigned website lets users interactively search for templates, cluster them by sequence similarity, structurally compare alternatives, and select which to use. When multiple templates are available, a user-guided selection step allows building models in different functional states. This made high-quality, complete structural modelling accessible without complex local software or large database downloads.