[gmx-users] How to choose the best pose of ligand from the trajectory file?

[Justin Lemkul]

On 12/25/14 5:03 PM, Hassan Aaryapour wrote:
> Dear Gromacs Users
>
> How can I find and score protein-ligand binding poses and choose the best
> pose or frame from the trajectory file after doing a Molecular dynamics
> simulation of 40ns?
>

"Best" is a qualitative assessment that should be driven by objective, 
quantitative metrics.  Decide how you want/need to analyze the interactions of 
the ligand with the protein, and the pose that is "best" is probably the one 
that captures most/all of the principle features (contacts, hydrogen bonds, 
dihedral angles, etc).

-Justin

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

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

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