[gmx-users] Protein preparation

Justin Lemkul jalemkul at vt.edu
Mon Mar 27 18:53:49 CEST 2017

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 



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


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