AMBER Archive (2009)

Subject: Re: [AMBER] Protein Docking

Date: Mon May 11 2009 - 15:33:15 CDT

Hi Lin,

if your ligand-protein conformation stays close to its initial value
during an MD run that's a good indication (but by no means a proof) that
it is a reasonable complex geometry and good for further study.

I would say that if you can show a stable complex rmsd during a
multi-nanosecond MD run, you can claim that your previous docking was
"successful", but there is no way besides some sort of empirical
verification to check that it also is correct, i.e. a complex geometry
occuring under physiological conditions.

Kind Regards,


On Mon, May 11, 2009 4:21 pm, Chih-Ying Lin wrote:
> HI
> When i visualize the MD trajectory, the protein and ligand are closed by.
> But, I don't know if ligand really DOCK on the protein.
> Please tell me how to define the successful docking.
> Thank you
> Lin
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Dr. Thomas Steinbrecher
BioMaps Institute
Rutgers University
610 Taylor Rd.
Piscataway, NJ 08854

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