Fig. 3. This figure presents a comparative illustration of workflows, challenges, objectives, and implementations across different geometry handling protocols. The ‘example’ column focuses on applications within the field of 3D molecular generation, while the ‘other models' column spans a broader range of geometry-centric topics. Key abbreviations include MG: Molecular Generation (without structures), S-MG: Structure-based Molecular Generation, CG: Conformation Generation (without structures), and S-CG: Structure-based Conformation Generation (also known as Docking).