Science

AutoDock is used to perform computational molecular docking of small molecules to proteins, DNA, RNA and other important macromolecules, by treating the ligand and selected parts of the target as conformationally flexible. It uses a scoring function based on the AMBER force field, and estimates the free energy of binding of a ligand to its target. Novel hybrid global-local evolutionary algorithms are used to search the phase space of the ligand-macromolecule system. We describe here the fundamental science that AutoDock is based on. Principles, laws and equations can be found in this section. We also present some applications of AutoDock from the published literature.