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 [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 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.
* [http://dock.compbio.ucsf.edu DOCK website]
* [http://dock.compbio.ucsf.edu/Online_Licensing/index.htm Licensing]
* 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]]
 
= General Overview =
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.
 
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]].


* Manual as a single PDF. [[Image:Dock61.pdf]]
= What Can DOCK Do for You =
* [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.
* [[FAQ]]


== New Features ==
We and others have used DOCK for the following applications:
The new features of DOCK 6 include:
* additional scoring options during minimization;
* [[DOCK 3.5.54]] scoring, including [[Delphi electrostatics]]
* [[ligand conformational entropy corrections]]
* [[ligand desolvation]]
* [[receptor desolvation]]
* [[Hawkins-Cramer-Truhlar GB/SA solvation scoring]] with optional [[salt screening]]
* [[PB/SA solvation scoring]]
* [[AMBER scoring]], including
  - [[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.
* 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 =


* [[Installing DOCK 6]]
* [[What does DOCK do?]]
* [[DOCK Accessories]]
* [[History of DOCK 6]]
* [[Command line arguments in DOCK6]]
* [[Ligand File Input]]
* [[Database Filter]]
* [[Orienting the Ligand]]
* [[Internal Energy Calculation]]
* [[Ligand Flexibility]]
* [[Scoring Functions in DOCK 6]]


[http://dock.compbio.ucsf.edu DOCK 6 website]
[[Category:DOCK]]
[[Category:DOCK 6]]
[[Category:Software]]
[[Category:Freecom]]

Latest 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).

General Overview

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.

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.

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

Retrieved from "http://wiki.docking.org/index.php?title=DOCK_6&oldid=11417"