Diffdock

This is a diffusion-based deep learning tool for molecular docking that predicts 3D binding poses of ligands to protein targets. You'd use it for structure-based drug design when you need to know where a molecule binds, not how strongly it binds. It handles PDB files or protein sequences via ESMFold, works with SMILES or structure files, and can process single complexes or batch virtual screening campaigns. The confidence scores tell you how certain the model is about the pose, not binding affinity, so you'll want to pair it with GNINA or MM/GBSA for affinity estimates. GPU recommended since it's 10-100x faster than CPU. First run takes a few minutes to pre-compute lookup tables.