DOCK 6: Difference between revisions

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* Manual as a single PDF. [[Image:Dock61.pdf]]
* Manual as a single PDF. [[Image:Dock61.pdf]]
* [http://dock.compbio.ucsf.edu/DOCK_6/tutorials/index.htm Tutorials] are available.
* [http://dock.compbio.ucsf.edu/DOCK_6/tutorials/index.htm Tutorials] are available.
* [[DOCK6:Tutorials]]
* [http://dock.compbio.ucsf.edu/Test_Sets/index.htm Test sets] are available.
* [http://dock.compbio.ucsf.edu/Test_Sets/index.htm Test sets] are available.
* [[FAQ]]
* [[DOCK6:Test sets]]
* [[DOCK:FAQ]]


== New Features ==
== New Features ==
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Because DOCK 6 is an extension of DOCK 5, it also includes all previous features.
Because DOCK 6 is an extension of DOCK 5, it also includes all previous features.


* [[DOCK:Introduction]]
* [[DOCK:Installation]]
* [[DOCK:Site preparation]]
* [[DOCK:Sampling]]
* [[DOCK:Scoring]]
* [[DOCK:Input]]
* [[DOCK:Output]]
* [[DOCK:Parameters]]
* [[DOCK:Parallelism]]
* [[DOCK:Accessories]]
* [[DOCK:File formats]]
* [[DOCK:References]]





Revision as of 00:23, 21 September 2007

DOCK 6 is a general purpose molecular docking program developed by the Kuntz Laboratory at UCSF. DOCK 6 (released summer 2006) is significant upgrade of DOCK 5 (released 2001-2006), which in turn was a complete rewrite and redesign of DOCK4 (released 1998), which itself was a complete re-design and re-write of DOCK 3.5 (released 1993-1994).

DOCK 6 is written in C++ and is functionally separated into independent components, allowing a high degree of program flexibility. Accessory programs are written in Fortran 77. We provide source code for all programs. The DOCK suite of programs requires on the order of 50 Mb of disk space and 48 Mb RAM.

New Features

The new features of DOCK 6 include:

 - receptor flexibility
 - the full AMBER molecular mechanics scoring function with
    + implicit solvent
    + conjugate gradient minimization
    + and molecular dynamics simulation capabilities.

Because DOCK 6 is an extension of DOCK 5, it also includes all previous features.


DOCK 6 website