Observational analysis reveals notable differences in predicted protein-protein complex interfaces, highlighting limitations of generative models in bioinformatics.
PLI-Analyzer is a computational tool for detailed analysis of protein, RNA, and DNA interaction interfaces, combining atomic-level contact detection with domain annotations from UniProt and InterPro. It offers customizable interaction thresholds, residue-level output, and compatibility with AI-generated structures, enabling precise validation and interpretation of contact dynamics. We applied PLI-Analyzer to evaluate high-quality protein-protein complexes predicted by AlphaFold-3 and Boltz-2, revealing notable differences in predicted interfaces and confidence scores. These findings highlight current limitations in generative structure models specifically for macromolecular complexes and underscore the need for robust, domain-informed evaluation frameworks in structural bioinformatics.
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Liang et al. (2025) studied this question.
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