DOCK 6: Difference between revisions

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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 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 [[DOCK 4]] (released 1998), which itself was a complete re-design and re-write of [[DOCK 3.5]] (released 1993-1994).


DOCK 6 is coded mostly in C++ and is functionally separated into independent components, allowing a high degree of program modularity and flexibility. Accessory programs are mostly 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 256 MB RAM. Some runs may require considerably more disk space.
DOCK 6 is coded mostly in C++ and is functionally separated into independent components (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 256 MB RAM. Some runs may require considerably more disk space.


* [[DOCK6:Tutorials]]
* [http://dock.compbio.ucsf.edu Official DOCK website]
* [[DOCK6:Test sets]]
* [http://dock.compbio.ucsf.edu/Online_Licensing/index.htm Licensing] (allow up to 7 days for reply)
* Manual as a single PDF. [[Image:Dock61.pdf]]
* [http://dock.compbio.ucsf.edu/DOCK_6/tutorials/index.htm Tutorials]
* [http://dock.compbio.ucsf.edu/Test_Sets/index.htm Test sets]
* [[DOCK:FAQ]]
* [[DOCK:FAQ]]
> OLD VERSIONS
* 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/Test_Sets/index.htm Test sets] are available.


== New Features ==
= New Features in DOCK 6 =
The new features of DOCK 6 include:
* additional scoring options during minimization;
* additional scoring options during minimization;
* [[DOCK 3.5.54]] scoring, including [[Delphi electrostatics]]
* [[DOCK 3.5.54]] scoring, including [[Delphi electrostatics]]
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     + and [[molecular dynamics simulation]] capabilities.
     + and [[molecular dynamics simulation]] capabilities.


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


* [[DOCK:Introduction]]
* [[DOCK:Introduction]]
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* [[DOCK:File formats]]
* [[DOCK:File formats]]
* [[DOCK:References]]
* [[DOCK:References]]
[http://dock.compbio.ucsf.edu DOCK 6 website]


[[Category:DOCK]]
[[Category:DOCK]]
[[Category:Portal]]
[[Category:Portal]]

Revision as of 07:41, 30 November 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 DOCK 4 (released 1998), which itself was a complete re-design and re-write of DOCK 3.5 (released 1993-1994).

DOCK 6 is coded mostly in C++ and is functionally separated into independent components (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 256 MB RAM. Some runs may require considerably more disk space.

New Features in DOCK 6

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

Manual