LigandMPNN
Inverse folding that is aware of ligands, nucleotides and metals.
Developer: Justas Dauparas, Institute for Protein Design, University of Washington
Overview
- Developer
- Justas Dauparas, Institute for Protein Design, University of Washington
- Commercial rights
- Commercial OK
- Commercial cost
- Free commercially
- Compute
- Single GPU
- Open weights
- Yes
- Last verified
Capabilities
Inverse folding that sees the non-protein context. Input: a PDB containing the protein plus ligands, nucleotides, metals or waters; output: sequences designed around that context, with side-chain packing - the right choice for binding pockets and metal sites.
When to use it
Use instead of ProteinMPNN when the binding site contains a small molecule, nucleic acid or metal that must be respected. Overkill for plain protein-protein interfaces.
Input / Output
- Input
- a PDB containing the protein plus ligands, nucleotides, metals or waters
- Output
- sequences designed around that context, with side-chain packing - the right choice for binding pockets and metal sites
Compute
Single GPU. Other tools with this compute profile →
Commercial Licensing
Commercial rights — may a company use it?
Commercial use OKLicence as writtenMIT License
MIT LICENSE file in the repo; no field-of-use restriction.
The licence read at the source allows use by a company. Attribution or copyleft conditions may still apply — read the note.
Commercial cost — is commercial use free of charge?
Free for commercial useNothing to pay: the licence read at the source grants commercial use with no fee, and the code and weights are public downloads. You still pay for your own compute.
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/dauparas/LigandMPNN
- Licence sources
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