Autodock

AutoDock is a suite of automated docking tools. It is designed to predict how small molecules, such as substrates or drug candidates, bind to a receptor of known 3D structure. Current distributions of AutoDock consist of two generations of software: AutoDock 4 and Autodock Vina.

AutoDock 4 actually consists of two main programs:

1.  autodock: performs the docking of the ligand to a set of grids describing the target protein
2.  autogrid: pre-calculates these grid. 

Basically Autodock help us to build some particular molecule and do some docking to our molecule for example spinning, adding hydrogen bond and etc.

Meanwhile, Autodock Vina is a new generation of docking software from the Molecular Graphics Lab. It achieves significant improvements in the average accuracy of the binding mode predictions. Here are some screenshot example on the Autodock Vina:

AutoDock has applications in : X-ray crystallography structure-based drug design lead optimization virtual screening (HTS) combinatorial library design protein-protein docking chemical mechanism studies AutoDock 4 is free and is available under the GNU General Public License. AutoDock Vina is available under the Apache license, allowing commercial and non-commercial use and redistribution.