Systematic Evaluation of AlphaFold2 and OpenFold3 on Protein-Peptide Complexes (opens in new tab)

Protein-peptide interactions are important mediators of diverse biological processes. While deep learning has revolutionized protein structure prediction, comparative evaluation of these methods, specifically for protein-peptide complexes, remains an area of active investigation. Here, we present a systematic benchmarking of AlphaFold2 (AF2) and OpenFold3 (OF3) on a curated, non-redundant dataset of 271 protein-peptide complexes evaluated under CAPRI peptide criteria, partitioned into disorde...