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.
Stephan Watkins
Gesendet: Samstag, 24. Mai 2014 um 12:24 Uhr
Von: "Nidhi Katyal" <nidhikatyal1...@gmail.com>
An: "Discussion list for GROMACS users" <gmx-us...@gromacs.org>
Betreff: [gmx-users] binding sites with MD
Von: "Nidhi Katyal" <nidhikatyal1...@gmail.com>
An: "Discussion list for GROMACS users" <gmx-us...@gromacs.org>
Betreff: [gmx-users] binding sites with MD
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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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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https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
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