[gmx-users] Protein preparation

[Justin Lemkul]

On 3/30/17 9:59 AM, Quin K wrote:
> 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.
>

All of these things matter, and the influence of all of them are what go into 
properly conducting your research project.

-Justin

> 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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-- 
==================================================

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

==================================================