DOCK 6: Difference between revisions
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DOCK 6 is a general purpose [[molecular docking]] program developed by the [http://dock.compbio.ucsf.edu/Group/group.html 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 a general purpose [[molecular docking]] program developed by the [http://dock.compbio.ucsf.edu/Group/group.html 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). | ||
* [http://dock.compbio.ucsf.edu DOCK website] | * [http://dock.compbio.ucsf.edu DOCK website] | ||
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= General Overview = | = General Overview = | ||
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. | 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 [[Category:DOCK | here]]. | ||
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. | |||
= What Can DOCK Do for You = | = What Can DOCK Do for You = | ||
Revision as of 22:22, 10 January 2019
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 website
- Licensing
- Manual as a single PDF. File:Dock61.pdf
- Tutorials
- Test sets
- DOCK:FAQ
General Overview
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.
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.
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...