Provide a PDB ID or upload an experimental or predicted protein structure (PDB or mmCIF). Ligands and waters in the file are ignored; pockets are detected from protein atoms only, up to 20,000 heavy atoms.
An elastic-network model samples conformers along the lowest-frequency normal modes, so hinge and breathing motions can open sites that are closed in the input. Pockets are detected in every conformer, clustered across the ensemble, and ranked by crypticity (how much a site opens relative to the input), persistence, and druggability.
The alpha-sphere detector proposes sites only at concavities. The learned surface detector scores the whole probe-accessible surface and reaches sites the geometry discards; the fused option pools both and ranks them with the matching model. Surface detectors run on geometry alone and take several times longer.
Each site gets a cubic AutoDock Vina box around its centroid (equivalent-sphere radius plus padding) and a Boltz-2 pocket constraint on its lining residues, indexed into the chain sequences reported with it. A one-atom reference ligand at the top site is written for DrugFlow / SurfDock chaining.