Prodigy Binding Affinity Prediction
PRODIGY predicts binding affinity and dissociation constants for protein–protein complexes based on their 3D structures.
Overview
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.
Run Prodigy Binding Affinity Prediction on Neurosnap
The Prodigy Binding Affinity Prediction online webserver allows anybody with a Neurosnap account to run and access Prodigy Binding Affinity Prediction, no downloads required. Information submitted through this webserver is kept confidential and never sold to third parties as detailed by our strong Terms of Use and Privacy Policy.
Features
- 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.
Statistics
Neurosnap periodically calculates runtime statistics based on job execution data. These estimates provide a general guideline for how long your job may take, but actual runtimes can vary significantly depending on factors like input size or settings used.
| Statistic | Value |
|---|---|
| Credit Usage Rate | loading... |
| Estimated Total Cost | loading... |
| Runtime Mean | loading... |
| Runtime Median | loading... |
| Runtime Standard Deviation | loading... |
| Runtime 90th Percentile | loading... |
| Runtime Longest | loading... |
API Request
Access Prodigy Binding Affinity Prediction using the Neurosnap API by sending a request using any programming language with HTTP support. To safely generate an API key, visit the API tab of your overview page.
Similar Tools
Explore tools with similar features, categories, and use cases.
Citations
Please cite the original work when using Prodigy Binding Affinity Prediction in publications or research outputs.
|
Vangone, A. and Bonvin, A. M. J. J. (2017). PRODIGY: A Contact-based Predictor of Binding Affinity in Protein-protein Complexes. Bio-protocol 7(3): e2124. DOI: 10.21769/BioProtoc.2124. |
|
Vangone, A., and Bonvin, A. M. J. J. (2015). Contacts-based prediction of binding affinity in protein-protein complexes. eLife 4: 291. |
|
Panagiotis L. Kastritis , João P.G.L.M. Rodrigues, Gert E. Folkers, Rolf Boelens, Alexandre M.J.J. Bonvin: Proteins Feel More Than They See: Fine-Tuning of Binding Affinity by Properties of the Non-Interacting Surface. Journal of Molecular Biology, 14, 2632–2652 (2014). (10.1016/j.jmb.2014.04.017) |
|
Neurosnap Inc. (2022). Neurosnap: An online platform for computational biology and chemistry. Available at: https://neurosnap.ai/ |