[gmx-users] Obtaining protein structure
Justin A. Lemkul
jalemkul at vt.edu
Thu Aug 25 18:51:39 CEST 2011
Steven Neumann wrote:
> Thank you for your help. I want to calculate binging free energy of
> small molecules to protein termini.
If you need high-quality structural data for disordered termini, you're unlikely
to get a good model without a huge amount of modeling, refinement, and
validation. As Mark said, there's good reason why structural information for
termini is hard to come by. You've posed a rather ill-defined task, so you'd do
well to invest some time in the literature for established procedures and means
of validation for your results.
> On Thu, Aug 25, 2011 at 4:22 PM, Mark Abraham <Mark.Abraham at anu.edu.au
> <mailto: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
>> <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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Justin A. Lemkul
ICTAS Doctoral Scholar
Department of Biochemistry
jalemkul[at]vt.edu | (540) 231-9080
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