[Dock-fans] metal-containing ligand

Scott Brozell sbrozell at scripps.edu
Mon May 7 16:27:51 PDT 2007


Hi,

This would also be a new frontier with Dock's Amber score.
However, it wouldn't be the wild wild west.

The type of role of the metal is important, e.g. electrostatic
versus chemical.  See these for more details and the general recipe:
http://blur.compbio.ucsf.edu/pipermail/dock-fans/2006-September/000723.html
http://blur.compbio.ucsf.edu/pipermail/dock-fans/2007-February/000896.html
One item these do not mention is that good GB radii might also be necessary.
Note this quickly becomes an Amber modeling exercise.

Scott

On Mon, 7 May 2007, John J. Irwin wrote:

>
> We have no experience docking metal containing ligands. The odds are
> certainly stacked against you, since most of the programs to prepare
> ligands are in general not parameterized for metals. Moreover, most
> docking scoring functions do not work well with metals, in my experience.
>
> Good luck.
>
> John
>
> John J. Irwin wrote:
> > Hi Agnes
> >
> > You might like to look at our paper: Irwin JJ, Raushel FM, Shoichet BK,
> > "Virtual screening against metalloenzymes for inhibitors and
> > substrates.", Biochemistry, 2005, 44(37),12316-28. DOI
> > <http://dx.doi.org/10.1021/bi050801k>.
> >
> > With Au, you may well have electronic effects that make the energetics
> > too subtle to be captured by classical mechanics approaches.
> >
> > Good luck!
> >
> > John
> >
> >
> > Simon Ágnes wrote:
> >
> >> I am wondering, if anyone has experience in docking metal-containing
> >> ligands, (by using any docking programs).
> >>
> >> In fact, my ligand contains gold  ( Au(I) ),  - so I would be greatful
> >> to hear of any docking program that could reliably treat my ligand.
> >>


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