[gmx-users] Obtaining protein structure

Justin A. Lemkul jalemkul at vt.edu
Thu Aug 25 17:20:34 CEST 2011

Steven Neumann wrote:
> Dear Gromacs Users,
> I want to do some simulations of the protein (its N anc C terminals) 
> which crystal structure does not exist. I submitted the sequence to 
> www.proteinmodelportal.org <http://www.proteinmodelportal.org/> 
> obtaining different structures based on different proteins from Protein 
> Data Bank. For instance my N terminal has 180 aa. Obtained models covers 
> %Seq id of 78% for 36 residues, 68% for 36 different residues, 62% of 36 
> another residues and many other models below 50%. The website provides 
> you with the PDB files of your query so sounds perfect as you do not 
> have to mutate every residue one by one.
> The question is whether this is efficent and provide a good result to 
> use such protein in my simualtions? Is this app. too big?
> What are the other ways to overcome this problem (obtain structure of 
> the protein which crystal structure does not exist?

Homology modeling is a field unto itself.  There are many programs that produce 
results with varying accuracy.  A quick look through some of the documentation 
from that site suggests there should be good feedback about the quality of the 

There are probably other forums better suited to these types of discussions. 
This mailing list is intended for Gromacs-related issues and usage.  Please bear 
that in mind.



Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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