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 <jalem...@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
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==================================================
Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow
Department of Pharmaceutical Sciences
School of Pharmacy
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University of Maryland, Baltimore
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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
jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul
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