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 DOCK4 (released 1998), which itself was a complete re-design and re-write of DOCK 3.5 (released 1993-1994). | ||
DOCK 6 is | 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. | ||
* [[DOCK6:Tutorials]] | |||
* [[DOCK6:Test sets]] | |||
* [[DOCK:FAQ]] | |||
> OLD VERSIONS | |||
* 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. | ||
* [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. | ||
== New Features == | == New Features == | ||
Revision as of 00:27, 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 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.
> OLD VERSIONS
- Manual as a single PDF. File:Dock61.pdf
- Tutorials are available.
- Test sets are available.
New Features
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.