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

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.