DOCK

Description

dock website

This module lets you use the software DOCK. DOCK addresses the problem of "docking" molecules to each other. In general, "docking" is the identification of the low-energy binding modes o f 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: http://dock.compbio.ucsf.edu/Old_Versions/index.htm 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: http://dock.compbio.ucsf.edu/DOCK_6/index.htm Modules system sets up the following environment variables for this module:

Environment Modules

Run module spider dock to find out what environment modules are available for this application.

Environment Variables

• HPC_DOCK_DIR - installation directory

Categories

chemistry