[gmx-users] Protein-Ligand Docking?

[Justin A. Lemkul]

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
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> First step, define what you mean by being "DOCKed".
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> Second step, determine if those conditions are meet by your protein and
> ligand.
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> Catch ya,
> 
> Dr. Dallas Warren
> Department of Pharmaceutical Biology and Pharmacology
> Pharmacy and Pharmaceutical Sciences, Monash University
> 381 Royal Parade, Parkville VIC 3010
> dallas.warren at pharm.monash.edu.au
> +61 3 9903 9167
> ---------------------------------
> When the only tool you own is a hammer, every problem begins to resemble
> a nail.
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-- 
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Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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