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 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: | |||
* 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. | |||
[http://dock.compbio.ucsf.edu DOCK 6 website] | [http://dock.compbio.ucsf.edu DOCK 6 website] | ||
Revision as of 18:20, 20 September 2006
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:
- 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.