Category:DOCK: Difference between revisions

This is the main page for documentation about DOCK.

main software distribute site: Dock web site

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.

The difference between the Docking category and the DOCK category is that DOCK is specific to our software, whereas Docking includes all docking programs and the approach in general.

There are 2 active versions and 3 available versions of DOCK.

• DOCK 3.7 which is the most recent in the DOCK 3 series. Actively developed.
• DOCK 6.6, which is the most recent in the DOCK 6 series. Actively developed.
• DOCK 4, a widely used version, but not actively developed.
• History of DOCK to explain why there are three versions of DOCK.