but using docking I have to fix the grid and have to dock at that position... which is not my objective ... I want the peptide to come and bind own its own to the protein... I have heard of full body dock , in which there is no need to define grid points , will that be useful ??<div>
<br><br><div class="gmail_quote">On Mon, Apr 11, 2011 at 2:02 PM, Thomas Evangelidis <span dir="ltr"><<a href="mailto:tevang3@gmail.com">tevang3@gmail.com</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex;">
You can try Rosetta for flexible peptide docking.<div><div></div><div class="h5"><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" target="_blank">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><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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