[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.


> Steven
> 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.
>     Mark
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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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