Contacts-based prediction of binding affinity in protein-protein complexes

Elife. 2015 Jul 20:4:e07454. doi: 10.7554/eLife.07454.


Almost all critical functions in cells rely on specific protein-protein interactions. Understanding these is therefore crucial in the investigation of biological systems. Despite all past efforts, we still lack a thorough understanding of the energetics of association of proteins. Here, we introduce a new and simple approach to predict binding affinity based on functional and structural features of the biological system, namely the network of interfacial contacts. We assess its performance against a protein-protein binding affinity benchmark and show that both experimental methods used for affinity measurements and conformational changes have a strong impact on prediction accuracy. Using a subset of complexes with reliable experimental binding affinities and combining our contacts and contact-types-based model with recent observations on the role of the non-interacting surface in protein-protein interactions, we reach a high prediction accuracy for such a diverse dataset outperforming all other tested methods.

Keywords: binding affinity; biophysics; buried surface area; non-interacting surface; none; protein contacts; protein–protein complexes; protein–protein interactions; structural biology.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Computational Biology / methods*
  • Molecular Biology / methods*
  • Protein Binding
  • Protein Interaction Maps*

Grants and funding

The funder had no role in study design, data collection and interpretation, or the decision to submit the work for publication.