Open-Source Molecular Docking and AI-Augmented Structure-Based Drug Design: Current Workflows, Challenges, and Opportunities

Molecular docking is a foundational technique in computational drug discovery, widely used to generate binding hypotheses, prioritize compounds, and support target-selectivity studies. The continued growth of open-source docking resources, together with improvements in scoring functions, sampling strategies, and hardware acceleration, has substantially lowered barriers to teaching, early-stage hit identification, and reproducible research. Beyond standalone docking engines, the open-source ecosystem now encompasses browser-accessible tools, preparation and analysis utilities, integrative modeling platforms, and AI-augmented methods for pose prediction, rescoring, and virtual screening. These developments have made docking workflows more accessible, customizable, and transparent across diverse research settings. This review examines open-source docking from a workflow-centered perspective, spanning study design, structural-data acquisition, binding-site definition, receptor and ligand preparation, docking execution, and post-docking validation. It further evaluates how open AI methods are being incorporated into these stages to expand structural coverage, improve screening efficiency, and support contemporary structure-based drug design. Collectively, this review outlines a practical and evidence-based framework for the effective use of open-source docking and virtual-screening pipelines in modern drug discovery.