[gmx-users] Protein-Ligand Docking?

[Dallas B. Warren]

Just as Mark and Justin have said, this is up to you to define this
question.

The reason I said that, is you were asking "how do I know if my molecule
is docked to the protein?".  The first step to answering that question
is defining what you mean by being docked.  Once you have a definition,
then you can look at your molecule / protein and see if it fulfills
those requirements.  I don't do docking, but from what I have seen is
that what is of interest is how well something fits into a pocket,
proximity to some groups, and interactions between the molecule and the
protein (hydrogen bonding and hydrophobic).

You really need to search the literature, as others will be doing
something similar.  And docking has been going on for a long time.

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
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When the only tool you own is a hammer, every problem begins to resemble
a nail.