Ya , I have tried with this server, but I am getting those residues whose side chains are present inside the barrel. Then in no way phosphate ion can bind to the barrel, as per the protein design rules..<br><br><div class="gmail_quote">
On Tue, May 31, 2011 at 1:33 AM, Francesco Oteri <span dir="ltr"><<a href="mailto:francesco.oteri@gmail.com">francesco.oteri@gmail.com</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex;">
<div bgcolor="#ffffff" text="#000000">
Dear bharat,<br>
you can try Phosfinder (<a href="http://phosfinder.bio.uniroma2.it" target="_blank">http://phosfinder.bio.uniroma2.it</a>). It is a
website that predict phosphate binding site on protein stucture.<br>
<br>
The paper url is:<a href="http://www.ncbi.nlm.nih.gov/pubmed/21622655" target="_blank">
http://www.ncbi.nlm.nih.gov/pubmed/21622655</a><br>
<br>
<br>
Il 31/05/2011 02:06, bharat gupta ha scritto:
<div><div></div><div class="h5"><blockquote type="cite">thanks ...<br>
<br>
<div class="gmail_quote">On Mon, May 30, 2011 at 5:03 PM, Justin
A. Lemkul <span dir="ltr"><<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</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><br>
<br>
bharat gupta wrote:<br>
<blockquote class="gmail_quote" style="margin:0pt 0pt 0pt 0.8ex;border-left:1px solid rgb(204, 204, 204);padding-left:1ex">
Well, mine is a beta-barrel protein called Green
Fluorescent Protein. In such a case the movement of ion is
very important. As the ion in side the barrel can quench
the fluorescence. That's what I want to track.. <br>
</blockquote>
<br>
</div>
You can probably address this with the methods I've described.
That's likely all that anyone can offer. Spend some time
looking through the literature at the many kinds of systems
that have been addressed using SMD and/or umbrella sampling
and come up with a coherent plan to address your system based
on what you find.
<div>
<div><br>
<br>
-Justin<br>
<br>
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<br>
Justin A. Lemkul<br>
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Department of Biochemistry<br>
Virginia Tech<br>
Blacksburg, VA<br>
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<a href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin" target="_blank">http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin</a><br>
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