Precision in Predicting Protein–Nucleic Acid Complexes: Establishing a Benchmark Data Set and Comparative Metrics

Protein-nucleic acid interactions are fundamental to biological processes and biotechnology, yet their computational prediction lags behind protein structure or protein-protein interaction modeling. This study introduces ProNASet, a benchmark data set of 100 experimentally resolved protein-nucleic acid complex structures, alongside a multidimensional evaluation framework using root mean square deviation (RMSD), TM-score, and local distance difference test (LDDT) metrics. We systematically evaluated four deep learning (DL) algorithms (AlphaFold3, Chai-1, HelixFold3, and Protenix) and two physically driven docking methods (HDOCK and HDOCK_NT). Our analysis revealed that physically driven methods significantly outperform current DL approaches in predicting protein-nucleic acid complex structures. The template-less HDOCK_NT demonstrated the highest success rate at 74.5% (using thresholds RMSD <2 Å, TM-score >0.9, and LDDT >0.6), compared to 63.8% for template docking and only 34.0% for the best-performing DL method, AlphaFold3. These results underscore the substantial need for improvement in DL methods for this specific task. The ProNASet benchmark provides a standardized testing platform, highlights intrinsic shortcomings in current DL models for capturing protein-nucleic acid interaction features, and guides the development of next-generation computational tools crucial for advancing genome editing and synthetic biology.