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Dear bharat,<br>
you can try Phosfinder (<a class="moz-txt-link-freetext" href="http://phosfinder.bio.uniroma2.it">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">
http://www.ncbi.nlm.nih.gov/pubmed/21622655</a><br>
<br>
<br>
Il 31/05/2011 02:06, bharat gupta ha scritto:
<blockquote
cite="mid:BANLkTimUvEPmDM1sK+NSXqRWxhyn7d8_zA@mail.gmail.com"
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 moz-do-not-send="true"
href="mailto:jalemkul@vt.edu">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 class="im"><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 class="h5"><br>
<br>
-Justin<br>
<br>
-- <br>
========================================<br>
<br>
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 moz-do-not-send="true" href="http://vt.edu"
target="_blank">vt.edu</a> | (540) 231-9080<br>
<a moz-do-not-send="true"
href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin"
target="_blank">http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin</a><br>
<br>
========================================<br>
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</blockquote>
</div>
<br>
<br clear="all">
<br>
-- <br>
Bharat<br>
Ph.D. Candidate<br>
Room No. : 7202A, 2nd Floor<br>
Biomolecular Engineering Laboratory<br>
Division of Chemical Engineering and Polymer Science<br>
Pusan National University<br>
Busan -609735<br>
South Korea<br>
Lab phone no. - +82-51-510-3680, +82-51-583-8343
<div>Mobile no. - 010-5818-3680<br>
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<br>
</blockquote>
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