Written and maintained by CASRAI Editorial Board
Last updated
SWISS-MODEL is a free-to-use web service for building a three-dimensional model of a protein from its amino acid sequence by homology modelling. This guide covers what it does, who runs it, its four modelling modes, how it relates to AlphaFold, and how to cite it. Facts are from the service’s own pages and its 2018 Nucleic Acids Research paper, read 2026-11-07.
What is SWISS-MODEL used for?
SWISS-MODEL describes itself as a web-based integrated service dedicated to protein structure homology modelling. Given a target sequence, it identifies suitable experimentally determined template structures, aligns the target to them, builds a model and evaluates the model’s quality. Researchers use it to get a structural model of a protein for which no experimental structure exists, provided a related template does.
The name is unrelated to football or to the Swiss-system tournament format. Searches that pair “SWISS-MODEL” with football are a naming collision; this page covers the bioinformatics tool only.
Who runs it and what it covers
SWISS-MODEL is developed by the Computational Structural Biology Group (Prof. Torsten Schwede) at the SIB Swiss Institute of Bioinformatics and the Biozentrum, University of Basel. The site lists ELIXIR and EU Horizon 2020 funding and presents it as part of SIB’s portfolio of open databases and software tools.
The 2018 paper describes the pipeline: template search with BLAST and HHblits, modelling of homo- and hetero-oligomeric complexes, the ProMod3 modelling engine, local quality estimation with QMEAN and QMEANDisCo, and a weekly-updated template library (SMTL). At the time of that paper, the SWISS-MODEL Repository held 1,067,355 models and 129,416 PDB structures mapped to UniProtKB. Today the Repository covers thirteen core species and is regenerated weekly from the latest UniProtKB proteome. AlphaFold DB structures are available as templates in the pipeline.
Four modelling modes in the interface
After the sign-in link (Log in / Create Account, top navigation), you work in myWorkspace through the Modelling menu. The documented modes are:
| Mode | You provide | Then |
|---|---|---|
| Automated Mode | A target sequence or a UniProtKB accession | Select Build Model |
| Alignment Mode | A target-template alignment (FASTA or Clustal) and a template by PDB ID, for example 1CNR_A | Build the model from your alignment |
| User Template | Your own template file, added with Add Template File… | Select Build Model |
| Project Mode | A DeepView project file | Continue modelling from the project |
A Modelling API with token authentication is also documented for scripted use. Before building a new model, check the Repository (/repository) to see whether your protein is already modelled.
SWISS-MODEL vs AlphaFold
The two are complementary rather than strictly competing. SWISS-MODEL is template-based: its output depends on a related experimental structure and the target-template alignment, and it reports quality estimates for the result. AlphaFold-style systems predict structure directly from sequence. Because AlphaFold DB structures can serve as templates within the SWISS-MODEL pipeline, a model can draw on both. See the CASRAI guides on the AlphaFold Protein Structure Database and ESMFold for the prediction side.
Strengths and limits
- Strength: a documented, end-to-end workflow (template search, alignment, building, quality evaluation) with several entry points, from a bare accession to your own alignment.
- Strength: a Repository of precomputed models, refreshed weekly, so many proteins need no new job.
- Limit: homology modelling needs a usable template; model reliability depends on the template and alignment, so inspect the quality estimates (QMEAN, QMEANDisCo) rather than treating a model as an experimental structure.
- Limit: an account is needed to work in myWorkspace.
Alternatives and companions
| Resource | Role relative to SWISS-MODEL | CASRAI guide |
|---|---|---|
| AlphaFold Protein Structure Database | Predicted structures; usable as templates in SWISS-MODEL | AlphaFold DB |
| ESMFold | Sequence-based structure prediction | ESMFold |
| UniProt | Source of sequences and accessions used as input | UniProt |
| InterPro | Domain and family annotation of your target | InterPro |
| ProtParam | Sequence-derived physicochemical properties | ProtParam |
How to cite SWISS-MODEL
The home page lists five publications; the general-purpose reference is Waterhouse A, et al. SWISS-MODEL: homology modelling of protein structures and complexes. Nucleic Acids Res. 2018;46(W1):W296-W303. doi:10.1093/nar/gky427. In methods text, also record the template identifiers and the model’s quality scores so the result is reproducible.
FAQ
What is the SWISS-MODEL used for?
Building 3D models of proteins from sequence by homology modelling, with template identification, alignment, model building and quality evaluation.
What is the SWISS-MODEL in football?
Nothing: it is a protein-modelling service and has no connection to football or tournament formats.
What are the key differences between SWISS-MODEL and AlphaFold?
SWISS-MODEL builds models from experimental templates via an alignment; AlphaFold predicts structure directly from sequence. AlphaFold DB structures are also available as templates inside SWISS-MODEL.
Is the SWISS-MODEL free?
The 2018 paper describes it as free to use. The site’s pages do not state pricing or licence and link to its Terms of use, which govern use.
Sources
- SWISS-MODEL home page and help documentation, read 2026-11-07.
- Waterhouse et al. 2018, Nucleic Acids Research, read 2026-11-07.
