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 -- ================================================== 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 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul ================================================== -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
