DOCK 6: Difference between revisions
(asd) |
No edit summary |
||
| Line 10: | Line 10: | ||
* [[DOCK:FAQ]] | * [[DOCK:FAQ]] | ||
= | = General Overview = | ||
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. | |||
= What Can DOCK Do for You = | |||
We and others have used DOCK for the following applications: | |||
*** | |||
*** | * predict binding modes of small molecule-protein complexes | ||
* | * search databases of ligands for compounds that inhibit enzyme activity | ||
* search databases of ligands for compounds that bind a particular protein | |||
* search databases of ligands for compounds that bind nucleic acid targets | |||
* examine possible binding orientations of protein-protein and protein-DNA complexes | |||
* help guide synthetic efforts by examining small molecules that are computationally derivatized | |||
* many more... | |||
= Manual = | = Manual = | ||
* [[DOCK | * [[Installing DOCK 6]] | ||
* [[DOCK | * [[History of DOCK 6]] | ||
* [[ | * [[Command line arguments in DOCK6]] | ||
* [[DOCK:Sampling]] | * [[DOCK:Sampling]] | ||
* [[DOCK:Scoring]] | * [[DOCK:Scoring]] | ||
Revision as of 22:29, 23 March 2016
DOCK 6 is a general purpose molecular docking program developed by the Kuntz Laboratory at UCSF. DOCK 6 (released summer 2006) replaced DOCK 5 (2001-2006), which is no longer available. DOCK 5 was a complete re-write of DOCK 4 (1998-2002), which itself was a complete re-design and re-write of DOCK 3.5 (released 1993-1994).
DOCK 6 is coded mainly in C++. Using the object oriented model, it is functionally separated into independent components (classes, methods), allowing a high degree of modularity and programming flexibility. Accessory programs are written in a variety of languages including C and Fortran 77. Source code is available for all programs. The DOCK suite of programs requires on the order of 50 MB of disk space and 512 MB RAM. Some runs may require considerably more disk space and more memory.
- DOCK website
- Licensing
- Manual as a single PDF. File:Dock61.pdf
- Tutorials
- Test sets
- DOCK:FAQ
General Overview
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.
What Can DOCK Do for You
We and others have used DOCK for the following applications:
- predict binding modes of small molecule-protein complexes
- search databases of ligands for compounds that inhibit enzyme activity
- search databases of ligands for compounds that bind a particular protein
- search databases of ligands for compounds that bind nucleic acid targets
- examine possible binding orientations of protein-protein and protein-DNA complexes
- help guide synthetic efforts by examining small molecules that are computationally derivatized
- many more...