[gmx-users] Obtaining protein structure

Mark Abraham Mark.Abraham at anu.edu.au
Thu Aug 25 17:22:47 CEST 2011

On 26/08/2011 1:16 AM, 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.

There will normally be reasons why the termini do not have a defined 
structure - often that this are in fact disordered. That will make your 
life doing simulations considerably more difficult, and not just in 
choosing a starting structure.

> 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?

Depends what simulations you plan - but very likely you will not be able 
to study more than one or two candidate structures.

> What are the other ways to overcome this problem (obtain structure of 
> the protein which crystal structure does not exist?

Protein structure prediction is a field all of its own for a reason. 
It's hard.

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