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) 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).
 
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.


* [http://dock.compbio.ucsf.edu DOCK website]
* [http://dock.compbio.ucsf.edu DOCK website]
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* [[DOCK:FAQ]]
* [[DOCK:FAQ]]


= New Features in DOCK 6 =
= General Overview =
* additional scoring options during minimization;
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 3]] scoring, including [[Delphi electrostatics]]
 
* [[ligand conformational entropy corrections]]
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]].
* [[ligand desolvation]]
 
* [[receptor desolvation]]
= What Can DOCK Do for You =
* [[Hawkins-Cramer-Truhlar GB/SA solvation scoring]] with optional [[salt screening]]
 
* [[PB/SA solvation scoring]]
We and others have used DOCK for the following applications:
* [[AMBER scoring]], including
 
** [[receptor flexibility]]
* predict binding modes of small molecule-protein complexes
** the full [[AMBER molecular mechanics scoring function]] with
* search databases of ligands for compounds that inhibit enzyme activity
*** [[implicit solvent]]
* search databases of ligands for compounds that bind a particular protein
*** [[conjugate gradient minimization]]
* search databases of ligands for compounds that bind nucleic acid targets
*** and [[molecular dynamics simulation]] capabilities.
* 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:Introduction]]
* [[Installing DOCK 6]]
* [[DOCK:Installation]]
* [[What does DOCK do?]]
* [[DOCK:Site preparation]]
* [[DOCK Accessories]]
* [[DOCK:Sampling]]
* [[History of DOCK 6]]
* [[DOCK:Scoring]]
* [[Command line arguments in DOCK6]]
* [[DOCK:Input]]
* [[Ligand File Input]]
* [[DOCK:Output]]
* [[Database Filter]]
* [[DOCK:Parameters]]
* [[Orienting the Ligand]]
* [[DOCK:Parallelism]]
* [[Internal Energy Calculation]]
* [[DOCK:Accessories]]
* [[Ligand Flexibility]]
* [[DOCK:File formats]]
* [[Scoring Functions in DOCK 6]]
* [[DOCK:References]]


[[Category:DOCK]]
[[Category:DOCK]]
[[Category:DOCK 6]]
[[Category:Software]]
[[Category:Software]]
[[Category:Freecom]]
[[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

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