Beyond rigid docking: deep learning approaches for fully flexible protein-ligand interactions

Sparked by AlphaFold2's groundbreaking success in protein structure prediction, recent years have seen a surge of interest in developing deep learning (DL) models for molecular docking. Molecular docking is a computational approach for predicting how proteins interact with small molecules known as ligands. It has become an essential tool in drug discovery, enabling structure-based virtual screening (VS) methods to efficiently explore vast libraries of drug-like molecules and identify potential therapeutic candidates. However, traditional docking methods primarily rely on search-and-score algorithms, which are computationally demanding. To be viable for VS applications, these methods often sacrifice accuracy for speed by simplifying their search algorithms and scoring functions. Recent advancements in DL have transformed molecular docking, offering accuracy that rivals-or even surpasses-traditional approaches while significantly reducing computational costs. Despite these advancements, DL-based molecular docking still faces major challenges. DL models often struggle to generalize beyond their training data and frequently mispredict key molecular properties, such as stereochemistry, bond lengths, and steric interactions, leading to physically unrealistic predictions. To overcome these limitations, a new generation of models is using DL to incorporate protein flexibility into docking predictions, aiming to more accurately capture the dynamic nature of biomolecular interactions-a long-standing challenge for traditional methods. This review explores how DL has reshaped molecular docking, examines its current shortcomings, and highlights emerging solutions. Finally, we discuss future opportunities to further bridge the gap between computational predictions and real-world molecular interactions.