- The most important feature of the new version of AutoDockTools helps users of AutoDock 4 to set up dockings with flexible sidechains in the receptor, but there are many new features, including support for the new formats used by AutoGrid 4 and AutoDock 4.
- The new version of AutoDock can dock ligands with more atom types than previous versions. To describe this larger number of atom types, we now use two characters instead of one. AutoDock 3 used the first character of the atom name to decide which atom type to used. The new version of AutoDock uses two-character atom types, that are now stored in a new input format for AutoDock and AutoGrid called PDBQT. This is very similar to the old PDBQ format.