PRODIGY: a web server for predicting the binding affinity of protein-protein complexes

Bioinformatics. 2016 Dec 1;32(23):3676-3678. doi: 10.1093/bioinformatics/btw514. Epub 2016 Aug 8.


Gaining insights into the structural determinants of protein-protein interactions holds the key for a deeper understanding of biological functions, diseases and development of therapeutics. An important aspect of this is the ability to accurately predict the binding strength for a given protein-protein complex. Here we present PROtein binDIng enerGY prediction (PRODIGY), a web server to predict the binding affinity of protein-protein complexes from their 3D structure. The PRODIGY server implements our simple but highly effective predictive model based on intermolecular contacts and properties derived from non-interface surface.

Availability and implementation: PRODIGY is freely available at: CONTACT:,

MeSH terms

  • Computational Biology / methods*
  • Internet*
  • Protein Binding
  • Protein Conformation
  • Protein Interaction Mapping / methods*
  • Software*