[gmx-users] Obtaining protein structure
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.
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