Ok. Thank you for your help. I will try to do it and see if it not too time consuming.<br clear="all"><div><br></div><div>--------------------------</div><br><div>Pierre THEVENET</div><div>Ph.D. Candidate</div><div>INSERM - MTi</div>
<div>Ecole Doctorale B3MI</div><div>Université Paris Diderot - Paris 7</div><div><br></div><br>
<br><br><div class="gmail_quote">2012/4/10 Justin A. Lemkul <span dir="ltr"><<a href="mailto:jalemkul@vt.edu">jalemkul@vt.edu</a>></span><br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<div class="im"><br>
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Pierre THEVENET wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
In most cases (it is form predicted structures) if the bonds is not formes, the S atoms are at the opposite side of the backbone. And I work on peptides, so the length of the structure isn't that big (50 residues max)<br>
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</blockquote>
<br></div>
Well, if you try the distance restraint approach, I'd do it in the absence of any solvent since there likely will be rather large structural changes (and thus very fast protein-solvent clashes as the restraints are satisfied), unless the peptide is pretty compact. Really short MD should tell you if this will even be feasible.<span class="HOEnZb"><font color="#888888"><br>
<br>
-Justin</font></span><div class="HOEnZb"><div class="h5"><br>
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Justin A. Lemkul<br>
Ph.D. Candidate<br>
ICTAS Doctoral Scholar<br>
MILES-IGERT Trainee<br>
Department of Biochemistry<br>
Virginia Tech<br>
Blacksburg, VA<br>
jalemkul[at]<a href="http://vt.edu" target="_blank">vt.edu</a> | <a href="tel:%28540%29%20231-9080" value="+15402319080" target="_blank">(540) 231-9080</a><br>
<a href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin" target="_blank">http://www.bevanlab.biochem.<u></u>vt.edu/Pages/Personal/justin</a><br>
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