Category:DOCK

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UCSF DOCK is a computer program for molecular docking, the process of orienting and scoring small molecules in a macromolecular (usually protein) binding site. Started in the early 1980s by Tack Kuntz and his group, DOCK was the first of many such programs, and has been in widespread use for over 30 years. All major pharmaceutical companies and most biomedical research universities run molecular docking screens in some form. The UCSF DOCK website is dock.compbio.ucsf.edu whence licenses are granted and software is distributed. There is a discussion group.

Available Versions

DOCK has been completely re-written twice, and substantially modified numerous times. Each re-write has not entirely superceded the previous version, and thus three versions continue to be available from UCSF. For the longer version of the history of DOCK, please see DOCK:History. The following versions are available:

  • DOCK 3.7 which is the most recent in the DOCK 3 series. Actively developed.
  • DOCK 6.7, 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 explains why there are three versions of DOCK, two of which are actively being developed.

More about DOCK

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.

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.

Subcategories

This category has the following 3 subcategories, out of 3 total.