[gmx-users] [gmx-user] MD simulation of protein-ligand complex

[Justin Lemkul]

On 12/24/19 12:47 PM, Quin K wrote:
> Hi
> Which of the following is the correct method to prepare a protein for
> docking and then for protein-ligand complex MD simulation?
>
> 1. Do an MD simulation of protein for 100 ns and use the structure of
> protein at 100 ns to do the protein-ligand MD simulation.

There is no guarantee that the final snapshot is in any way 
representative of the rest of the simulation, so this is basically an 
arbitrary choice.

> 2. Do an energy minimization of protein (like 5 ns) and use that structure
> for MD simulation of protein-ligand complex.

Energy minimization is not dynamical, so there are no time units. This 
is the more common approach (using an experimental structure) but is not 
necessarily representative of the dominant structure that exists in 
solution or that is receptive to ligand binding.

The better approach is to choose a representative snapshot (or multiple) 
from a long MD simulation with very careful analysis of local (binding 
site) and global (overall structure) properties. Then you can make a 
robust choice for a docking target (or multiple, depending on what you 
find).

-Justin

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Justin A. Lemkul, Ph.D.
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Virginia Tech Department of Biochemistry
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