A simple probabilistic AlphaFold interaction score
Publikation: Beitrag in Fachzeitschrift › Forschungsartikel › Beigetragen › Begutachtung
Beitragende
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
| Originalsprache | Englisch |
|---|---|
| Aufsatznummer | e70760 |
| Fachzeitschrift | Protein science |
| Jahrgang | 35 |
| Ausgabenummer | 9 |
| Publikationsstatus | Veröffentlicht - Sept. 2026 |
| Peer-Review-Status | Ja |
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