Foldseek
Fast structural similarity search across millions of structures.
Developer: Steinegger lab, Seoul National University
Overview
- Developer
- Steinegger lab, Seoul National University
- Category
- Data and structure resources
- Commercial rights
- Restricted
- Commercial cost
- Free commercially
- Compute
- CPU
- Open weights
- Yes
- Last verified
Capabilities
Structure search. Input: a query structure; output: structurally similar entries across PDB/AFDB with alignment and E-values - how you check whether a designed fold or epitope already exists.
When to use it
Use to find structural neighbours of a designed backbone, e.g. novelty checks and self-similarity screening. GPL copyleft makes embedding it in a closed product awkward.
Input / Output
- Input
- a query structure
- Output
- structurally similar entries across PDB/AFDB with alignment and E-values - how you check whether a designed fold or epitope already exists
Compute
Commercial Licensing
Commercial rights — may a company use it?
RestrictedLicence as writtenGNU General Public License v3.0
LICENSE.md in the repo is GPL-3.0. Internal commercial use is allowed, but distributing software that incorporates Foldseek requires releasing the derivative work under GPL-3.0, which matters if you plan to ship a product containing it.
Some commercial use is possible, but a component, dependency or condition needs a paid licence or carries obligations.
Commercial cost — is commercial use free of charge?
Free for commercial useNo fee, but GPL-3.0: if you ship Foldseek inside a product you distribute, you must release that product's source under GPL-3.0. Running it internally as a service carries no such obligation.
Price and rights are separate: this panel is about money, the panel above is about permission.
- Commercial OK ≠ Free of charge. A tool can be licensed for company use and still need a paid licence for a dependency (BindCraft → PyRosetta).
- Free download ≠ Commercially licensed. Weights you can download at no cost may still forbid commercial use (AlphaFold 3).
- Unverified ≠ Commercially permitted. If no published statement settles it, treat it as unknown — not as a yes.
- Every component counts. Each status considers the code licence, the model-weights terms, required dependencies and any terms of use.
Model Weights
Open weights. A separate weights licence is Not documented as its own field; where weights carry different terms from the code, that is stated in the licence explanation above.
Dependencies
Not documented as a separate field. Any dependency that affects commercial use (for example a paid PyRosetta licence) is named in the licence and cost explanations above.
Official References
- Official site / repo
- github.com/steineggerlab/foldseek
From the makers of FoldScout
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Get told when a licence changes
Licences on these tools do change. One short email when a status flips or a tool is added. No other use of your address.