[Dock-fans] constrained docking

[Scott Brozell]

Hi,

Piotr Cieplak wrote:
> I want to do constrained docking, e.g. keep some portion of the docked
> molecules in the same place (could move slightly) while the other part
> moves freely. For example - keep a single peptide bond or carboxy group
> in place, while the rest of the molecule could float in space.  Is it
> possible to do something like that with DOCK6.0?
> Thanks for any help with that.

One general feature of Dock that might have been able to
enable constrained docking:
http://dock.compbio.ucsf.edu/DOCK_6/dock6_manual.htm#ManualSpecificationofNonrotatableBonds
is not currently available:
http://blur.compbio.ucsf.edu/pipermail/dock-fans/2007-April/000982.html

Selecting parts of a molecule is possible with Amber score,
but Amber score does not yet support full fledged docking.

As an aside I recommend upgrading to dock 6.1:
http://dock.compbio.ucsf.edu/DOCK_6/6.1/new_in_6.1.txt

Scott