DOCK addresses the problem of "docking" molecules to each other. In general, "docking"
is the identification of the low-energy binding modes of
a small molecule, or ligand, within the active site of a macromolecule, or receptor, whose structure is known. A compound that interacts strongly with, or binds, a receptor associated with a disease may inhibit its function and thus act as a drug. Solving the docking problem computationally requires an accurate representation of the molecular energetics
as well as an efficient algorithm to search the potential
binding modes.
Historically, the DOCK algorithm addressed rigid
body docking using a geometric matching algorithm
to superimpose the ligand onto a negative image of
the binding pocket. Important features that improved the algorithm's ability to find the lowest-energy binding mode, including force-field based scoring, on-the-fly optimization, an improved matching algorithm
for rigid body docking and an algorithm for
flexible ligand docking, have been added over the years. For more information on past versions of DOCK, click here.
With the release of DOCK 6, we continue to improve the algorithm's ability to predict binding poses by adding new features like force-field scoring enhanced by solvation and receptor flexibility. For more information about the current release of DOCK, click here.
This image graphically depicts a typical DOCK setup used toward the discovery of a potential disease inhibitor. The target (green) is an HIVgp41 protein, which mediates membrane fusion between the HIV virus and the host cell. During DOCKing, spheres (orange) are used to guide the placement of potential compounds (colored by atom type). These compounds are then scored using a grid (gray box) and ranked by their potential to bind to the target. (Courtesy of Dr. Robert Rizzo) 
