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.
-Justin
Steven
On Thu, Aug 25, 2011 at 4:22 PM, Mark Abraham <mark.abra...@anu.edu.au
<mailto:mark.abra...@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
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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