You can try Rosetta for flexible peptide docking.<br><br><br><div class="gmail_quote">On 11 April 2011 15:32, Mark Abraham <span dir="ltr"><<a href="mailto:Mark.Abraham@anu.edu.au">Mark.Abraham@anu.edu.au</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;"><div class="im"><blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;">
Hi,<br>
<br>
I want to know how can I predict where a designed peptide will bind to my protein target or not using simulation ... Can anybody guide me ??<br>
</blockquote>
<br></div>
I don't think anybody has the computational resources to answer this question with unguided MD. Docking programs are probably the way to get a guide about what binding modes might be reasonable, but I don't know what software might be fit for the purpose.<br>
<br>
Mark<br><font color="#888888">
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<p style="margin-bottom: 0cm;" align="LEFT">Thomas Evangelidis</p>
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