[gmx-users] Obtaining protein structure

[Steven Neumann]

Thank you for your help. I want to calculate binging free energy of small
molecules to protein termini.

Steven

On Thu, Aug 25, 2011 at 4:22 PM, Mark Abraham <Mark.Abraham at anu.edu.au>wrote:

>  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 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.
>
> Mark
>
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