[gmx-users] binding sites with MD

Justin Lemkul jalemkul at vt.edu
Sat May 24 13:36:00 CEST 2014

On 5/24/14, 6:24 AM, Nidhi Katyal 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.

It's possible, but at such large ligand:protein ratios, you'll probably get a 
lot of nonspecific binding, and the interactions could be getting stuck in local 
minima, so you need some way of scoring the outcome based on energy.



Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441


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