[gmx-users] Protein preparation

[Quin K]

Thank you.

There are so many pdb structures for the protein I'm looking for.
I'm not sure which one to pick.
What should I look for when picking a protein pdb structure?
I want to test for an inhibitor with the protein.
Which of the following I should look for.

Resolution
Ligands
Inhibitors attached vs Not attached.
Correct sequence of residues
Ions present
Co-factors present ? etc.

Thanks.

Regards
Quin.


On Mon, Mar 27, 2017 at 10:23 PM, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> On 3/27/17 2:16 AM, Rasika Kelum wrote:
>
>> Thank you Justin. Highly appreciate your help.
>>
>> If there are missing residues, any suggestions on fixing the protein?
>>
>>
> There are plenty of tools to do that; Modeller is one of them.
>
> 1. How to find correct sequence? (is there any website to find correct
>> sequence?)
>>
>
> This should be your first stop in starting your research.  If you don't
> know the sequence or other very fundamental information, stop what you're
> doing at the terminal and pull out the biology literature.
>
> 2. How to FIX the sequence (using what software?)
>>
>
> See above.
>
> 3. Once residues are fixed how would that affect the geometry of the
>> protein? Do we have to fix the geometry of protein as well?
>>
>>
> Depends on the quality of the reconstruction of missing atoms.  Most
> programs are pretty robust, but a very short energy minimization usually
> relaxes away any problems.
>
> -Justin
>
> --
> ==================================================
>
> 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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