Proteome scale drug prioritization from AlphaFold 3 interaction confidence

Authors

Akabari, R., Mangione, W., Falls, Z., Samudrala, R.

Abstract

AlphaFold 3 (AF3) predicts protein ligand complexes, but the utility of its confidence scores for drug prioritization remains unclear. We benchmarked AF3 interaction scores against BANDOCK+, an experimentally informed approach, using approved drugs and human protein libraries. AF3 ipTM achieved similar aggregate disease ranking performance to BANDOCK+, with differences among individual indications. These results support the evaluation of AF3 interaction confidence as a source of information for proteome scale drug prioritization.

Preprint server: bioRxiv
The authors list and abstract were imported from bioRxiv on 21 Oct 2026.

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