PRODIGY
Estimates binding affinity of protein-protein complexes from structure.
Developer: Bonvin lab, Utrecht University
Overview
- Developer
- Bonvin lab, Utrecht University
- Category
- Docking and affinity estimation
- Commercial rights
- Commercial OK
- Commercial cost
- Free commercially
- Compute
- CPU
- Open weights
- Yes
- Last verified
Capabilities
Affinity estimate for a protein-protein complex. Input: a complex structure (PDB); output: a predicted binding affinity (dG/Kd estimate) from interfacial contact composition - a structure-based ranking signal, not a measurement.
When to use it
Fast contact-based ΔG estimate to rank protein-protein complexes. It was fitted on experimental crystal complexes, so predictions on modelled or designed interfaces are rough at best and never a substitute for SPR/BLI.
Input / Output
- Input
- a complex structure (PDB)
- Output
- a predicted binding affinity (dG/Kd estimate) from interfacial contact composition - a structure-based ranking signal, not a measurement
Compute
Commercial Licensing
Commercial rights — may a company use it?
Commercial use OKLicence as writtenApache License 2.0
Apache-2.0 LICENSE file reported by the GitHub license API for haddocking/prodigy.
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/haddocking/prodigy
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