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On 26/08/2011 1:16 AM, Steven Neumann wrote:
<blockquote
cite="mid:CAKZJqQFqyBN_=o=ALixnj_UJoDL9S5cH5b=JdBjNqcmA3UFjQA@mail.gmail.com"
type="cite">
<div>Dear Gromacs Users,</div>
<div> </div>
<div>I want to do some simulations of the protein (its N anc C
terminals) which crystal structure does not exist.</div>
</blockquote>
<br>
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.<br>
<br>
<blockquote
cite="mid:CAKZJqQFqyBN_=o=ALixnj_UJoDL9S5cH5b=JdBjNqcmA3UFjQA@mail.gmail.com"
type="cite">
<div> I submitted the sequence to <a moz-do-not-send="true"
href="http://www.proteinmodelportal.org/">www.proteinmodelportal.org</a>
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. </div>
<div>The question is whether this is efficent and provide a good
result to use such protein in my simualtions? Is this app. too
big? </div>
</blockquote>
<br>
Depends what simulations you plan - but very likely you will not be
able to study more than one or two candidate structures.<br>
<br>
<blockquote
cite="mid:CAKZJqQFqyBN_=o=ALixnj_UJoDL9S5cH5b=JdBjNqcmA3UFjQA@mail.gmail.com"
type="cite">
<div>What are the other ways to overcome this problem (obtain
structure of the protein which crystal structure does not exist?</div>
</blockquote>
<br>
Protein structure prediction is a field all of its own for a reason.
It's hard.<br>
<br>
Mark<br>
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