[gmx-users] Mycobacterium cell wall protein

[Justin Lemkul]

On 1/9/17 2:09 AM, Shanmuga Priya V.G wrote:
> Dear Gromacs Users,
> I have a insilico model of Mycobacterium tuberculosis cell wall  (surface)
> protein
> which has no transmembrane helices. Which Gromacs tutorials should I
> follow for MD studies to know about its conformational stability and
> latter for protein - ligand studies. Kindly guide me
>

This depends on whether or not the protein has any significant interaction with 
the cell wall.  If it does, you'll have to model it as a peripheral membrane 
protein (e.g. bound to, but not embedded in, the membrane).  Otherwise, if it is 
distant from the cell wall, it's like any normal protein-in-water system or 
protein-ligand complex, for which any number of tutorials exist (just ask Google!).

-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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