Docking with the AutoDock Suite
Computational docking is widely used for study of protein-ligand interactions and for drug discovery and development. Typically the process starts with a target of known structure, such as a crystallographic structure of an enzyme of medicinal interest. Docking is then used to predict the bound conformation and binding free energy of small molecules to the target. Single docking experiments are useful for exploring the function of the target, and virtual screening, where a large library of compounds are docked and ranked, may be used to identify new inhibitors for drug development.
AutoDock is a suite of free open–source software for the computational docking and virtual screening of small molecules to macromolecular receptors. The suite currently includes several complementary tools:
Computational Docking Software
Autodock4 is a computational docking program based on an empirical free energy force field and rapid Lamarckian genetic algorithm search method. It is effective for general-purpose docking of ligands to biomolecular targets and virtual screening, and specialized functions are available for prediction of covalent ligand complexes, ligands with flexible rings, explicit hydration, and metalloprotein targets.
AutoDock Vina is a turnkey computational docking program based on a simple scoring function and rapid gradient-optimization conformational search. It is fast and effective for docking of drug-like ligands to protein targets.
AutoDockFR is a computational docking program with flexible protein targets, including sidechain motion and induced fit.