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<div>Theres one paper that shows (VMD film) and talks about diffusion times I know of, however I do not know of any simply looking for ligands via setting up an MD system, then running them long enough to see if they find a site, this seems like a large amount of excessive work as the systems are much more complicated, and require much more computer power. Usually the rule of thumb in the process is to first do massive amounts of docking, and then move to MD to validate suspected sites. This may be a preference as several strategies are published approaching this.</div>
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<div>Stephan Watkins</div>
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<div style="margin:0 0 10px 0;"><b>Gesendet:</b> Samstag, 24. Mai 2014 um 12:24 Uhr<br/>
<b>Von:</b> "Nidhi Katyal" <nidhikatyal1989@gmail.com><br/>
<b>An:</b> "Discussion list for GROMACS users" <gmx-users@gromacs.org><br/>
<b>Betreff:</b> [gmx-users] binding sites with MD</div>
<div name="quoted-content">Hi all,<br/>
<br/>
I would like to ask if unbiased MD in nanoseconds time scale be used to<br/>
find the potential binding sites of ligand with protein?<br/>
<br/>
I have simulated for 50ns, 1:14 and 1:24 protein:ligand simultaneously with<br/>
random placement of ligand initially. In the time interval between 40 to<br/>
50ns, movement of ligand molecules can be seen around certain sites only<br/>
for both the runs. Can these sites be considered as binding sites? Also,<br/>
ligand molecules are involved in both hydrophobic and hydrogen bonding<br/>
interactions with these sites.<br/>
<br/>
Thanks in advance.<br/>
--<br/>
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