Comprehensive evaluation of artificial intelligence-empowered approaches for protein–aptamer complex prediction

Drug discovery is a time-consuming, expensive, and high-risk process. Recent advances in artificial intelligence (AI) have enabled major breakthroughs in small-molecule and protein therapeutics. However, AI-driven design of aptamer drugs remains largely unexplored. Aptamers are short (15-100 nt) single-stranded DNAs or RNAs that exhibit high binding affinity, high specificity, and low immunogenicity, making them promising candidates for disease (such as cancer) therapeutics. Compared with protein-ligand or protein-protein systems, protein-aptamer complexes are under-represented in public structural databases, and aptamers themselves are highly flexible and relatively large molecules. These characteristics present distinct challenges for AI-based structural modeling. Here, we systematically evaluate recent AI frameworks, including AlphaFold3, Chai-1, Boltz-2, and RoseTTAFold2NA, along with a template-based approach, in predicting protein-aptamer complex structures and estimating binding free energies. We establish an independent benchmark to assess their performance in structural accuracy, stability, and energetic consistency. This study provides a foundation for the application of AI in aptamer drug design and offers a reference framework for future research in nucleic-acid therapeutics and biomolecular modeling.