GOLD

High-precision grid-based docking with hierarchical filtering. Glide WS (2025) explicitly models water molecules during docking.

Diffusion-based generative model that treats docking as a generative problem over ligand poses. No pre-specified binding pocket needed.

AutoDock Vina-based docking engine augmented with a 3D CNN scoring function. Uses Vina for sampling, CNN for scoring and re-ranking.

Geometric flow matching model that maps apo protein structures to bound complexes for multiple ligands simultaneously. Outputs confidence scores and affinity estimates.