[gmx-users] binding sites with MD

[Nidhi Katyal]

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.