Prodigy Binding Affinity Prediction
PRODIGY predicts binding affinity and dissociation constants for protein–protein complexes based on their 3D structures.
PRODIGY (PROtein binDIng enerGY prediction) is a computational tool for predicting the binding affinity of protein–protein complexes using their 3D structures. Leveraging an efficient contact-based approach, PRODIGY estimates binding free energy and dissociation constants while providing insights into structural determinants of protein interactions. By combining interfacial contact properties with non-interacting surface features, PRODIGY delivers reliable predictions critical for understanding molecular interactions, guiding therapeutic development, and engineering protein complexes.
Estimated resource cost: 0.000062
Categories: Molecular Docking & Interactions
Tags: Affinity Prediction Developability Proteins
Key Capabilities
- Accepts 3D structural input of protein–protein complexes in PDB format.
- Calculates binding free energy (∆G) and dissociation constant (Kd) based on interfacial contact analysis.
- Provides a detailed report, including the number and type of intermolecular contacts, percentage of charged and polar residues, and residue-specific interactions.
Runtime Statistics
| Metric | Value |
|---|---|
| runtime_mean | 3 |
| runtime_median | 4 |
| runtime_std | 5 |
| runtime_90th_percentile | 5 |
| runtime_max | 315 |
Similar Tools
- FlowDock
- AF2Bind
- AllMetal3D
- AutoDock Vina (smina)
Ready to submit your job?
Review your configuration, then confirm the estimated credit cost before you run the job. Note that credit estimates are not guaranteed and runtime can vary depending on inputs and settings.
Estimated Credits: 0.000062
Invite-only, limited-time access. Please contact ztang@getantibody.com.
Invite-only, limited-time access. Please contact ztang@getantibody.com.