A simple probabilistic AlphaFold interaction score

Publikation: Beitrag in Fachzeitschrift › Forschungsartikel › Beigetragen › Begutachtung

Beitragende

  • Mihaly Badonyi - , Max-Planck-Institut für molekulare Zellbiologie und Genetik, Max-Planck-Institut für Physik komplexer Systeme, Zentrum für Systembiologie Dresden (CSBD) (Autor:in)
  • Agnes Toth-Petroczy - , Exzellenzcluster PoL: Physik des Lebens, Max-Planck-Institut für molekulare Zellbiologie und Genetik, Zentrum für Systembiologie Dresden (CSBD) (Autor:in)

Abstract

AlphaFold has enabled large-scale prediction of protein–protein and protein–nucleic acid complexes, but ranking and assessing the quality of predicted models remain challenging. Existing confidence scores are often highly parametrized and provide limited interpretability. We introduce a simple geometric framework that converts AlphaFold-predicted aligned error (PAE) into conditional contact probability. We show that these probabilities are well calibrated to the fraction of native contacts observed across experimentally determined structures. Motivated by this, we define the Pinc score (Probability of interface native contacts) as the mean contact probability between interacting chains. Because the probabilistic interpretation extends to individual residues, Pinc captures local structural constraint beyond interfacial burial, enabling residue-level prioritization of hotspot positions for mutational studies. Depending solely on a single empirically fixed contact radius, Pinc offers an interpretable path from PAE to interface confidence, matching or exceeding the classification performance of more complex methods across five independent benchmark sets. We provide a portable, dependency-free C program and a Google Colab notebook for calculating Pinc scores for AlphaFold models at https://git.mpi-cbg.de/tothpetroczylab/Pinc.

Details

OriginalspracheEnglisch
Aufsatznummere70760
FachzeitschriftProtein science
Jahrgang35
Ausgabenummer9
PublikationsstatusVeröffentlicht - Sept. 2026
Peer-Review-StatusJa

Externe IDs

PubMed 42615564

Schlagworte

ASJC Scopus Sachgebiete

  • Biochemie - alphafold, computational biology, protein complexes, protein structure modeling, protein–DNA interaction, protein–protein interaction prediction, software
  • Molekularbiologie - alphafold, computational biology, protein complexes, protein structure modeling, protein–DNA interaction, protein–protein interaction prediction, software

Schlagwörter

  • alphafold, computational biology, protein complexes, protein structure modeling, protein–DNA interaction, protein–protein interaction prediction, software