[gmx-users] Protein-Ligand Docking?

[Chih-Ying Lin]

Hi
1. If any one know the related paper of protein-ligand docking using
MD, please refer to to those papers.

2. from Justin =>
"we often start with a protein-ligand complex for which we know the position and
orientation of some inhibitor, usually from X-ray diffraction data.  We test our
model to see if we can replicate that interaction and then use those parameters
to attempt similar associations with other compounds."

=>do you mean that we can mimic  X-ray diffraction experimental data
from MD simulation?

=> what are "those parameters"?


3. I have been given the protein and the surfactant and tried to "see"
if  the surfactant will dock on the protein. => what is the next step
that I can do?


Thank you very much
Lin






Chih-Ying Lin wrote:
> HI
> Would you please give me an example of "definition" of DOCKed?
>

You have to have some criteria to start with.  When we do true docking, we often
start with a protein-ligand complex for which we know the position and
orientation of some inhibitor, usually from X-ray diffraction data.  We test our
model to see if we can replicate that interaction and then use those parameters
to attempt similar associations with other compounds.

The bottom line is - you have to know what you are looking for.  What residues
should be involved in the interaction (some known catalytic or binding site),
and should the interaction even occur under relevant conditions?  If you don't
know what you might be looking for, you will have a hard time convincing anyone
that your results are meaningful.

-Justin

> Thank you
> Lin
>