What is "AutoDock"?

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To quote from the official website:
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.

AutoDock actually consists of three separate programs:

  1. AutoDock performs the docking of the ligand to a set of grids describing the target protein
  2. AutoGrid pre-calculates these grids
  3. AutoTors sets up which bonds will be treated as rotatable in the ligand.

AutoDock has been widely used and there are many examples of its successful application in the literature (see References). It is very fast, provides high quality predictions of ligand conformations, and good correlations between predicted inhibition constants and experimental ones. For a more complete list, see the official AutoDock homepage and click on "capabilities".