[gmx-users] binding sites with MD

[Michael Shirts]

Look for papers by D. E. Shaw and Gianni di Fabritiis.  They have done
this, but it generally takes at least microseconds or milliseconds to
converge.

On Sat, May 24, 2014 at 6:24 AM, Nidhi Katyal <nidhikatyal1989 at gmail.com> wrote:
> Hi all,
>
> I would like to ask if unbiased MD in nanoseconds time scale be used to
> find the potential binding sites of ligand with protein?
>
> I have simulated for 50ns, 1:14 and 1:24 protein:ligand simultaneously with
> random placement of ligand initially. In the time interval between 40 to
> 50ns, movement of ligand molecules can be seen around certain sites only
> for both the runs. Can these sites be considered as binding sites? Also,
> ligand molecules are involved in both hydrophobic and hydrogen bonding
> interactions with these sites.
>
> Thanks in advance.
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