AutoDock was the first docking program to model the ligand with full conformational flexibility. The first version was written in Prof. Arthur J. Olson's Laboratory in 1989-1990, in FORTRAN-77, by Dr. David S. Goodsell. (It was nearly called AutoDoq, since it used quaternions to perform rotations; quaternions do not suffer from the so-called gymbal lock problem associated with Euler angles.)
The second version was made more portable and modular, being written in C by Dr. Garrett M. Morris beginning in 1991, adding new features, documentation and examples, and introducing parallel docking using clusters of computers.
The third version was written by Dr. Morris and Scott Halliday in C and C++, with the introduction of new and more powerful search methods (due to Dr. William Hart and Dr. Rik Belew) and a combined molecular mechanics/linear free energy model that estimates the free energy change upon ligand-protein binding to within about 2.1 Kcal/mol (work carried out by Dr. Morris, and inspired by that of Dr. Hans-Joachim Böhm).
AutoDock 4 introduces the ability to model conformational flexibility in selected sidechains in the target macromolecule; it uses a new desolvation energy term, and is calibrated on a set of 188 ligand-protein complexes of known structure and binding affinity. There have been numerous improvements made to the search algorithms and the molecular representation of the problem, and AutoDock supports more atom types than previous versions. Thanks to ADT, a very refined graphical user interface, AutoDock has been made easier to use than earlier versions, allowing bench chemists and other non-computational chemists to set up dockings and analyse the results visually.