<div>Hi</div>
<div> I have used TANGO Aggrescan, Zyggregator and other online tools but I am unable to find and pinpoint residue responsible for aggregation. Then I did MD simulation of the proteins with gromacs at different temperature. Now in this background I need suggestion to analyse my MD trajectory.</div>
<div>shahid Nayeem<br><br> </div>
<div><span class="gmail_quote">On 5/12/10, <b class="gmail_sendername">Ran Friedman</b> <<a href="mailto:r.friedman@bioc.uzh.ch">r.friedman@bioc.uzh.ch</a>> wrote:</span>
<blockquote class="gmail_quote" style="PADDING-LEFT: 1ex; MARGIN: 0px 0px 0px 0.8ex; BORDER-LEFT: #ccc 1px solid">Hi,<br><br>There's no recipie to locate aggregation hot spots based on MD<br>simulations. There are many papers on simulations of protein and peptide<br>
aggregation from which you can draw some ideas, but bear in mind that<br>aggregation of more than very few and very small peptides is typically<br>much slower than what one can simulate using atomistic MD.<br><br>For a quick approach you can use sequence analysis tools, e.g., TANGO<br>
<a href="http://tango.crg.es/">http://tango.crg.es/</a><br><br>Good luck,<br>Ran<br><br>--<br>------------------------------------------------------<br>Ran Friedman<br>Postdoctoral Fellow<br>Computational Structural Biology Group (A. Caflisch)<br>
Department of Biochemistry<br>University of Zurich<br>Winterthurerstrasse 190<br>CH-8057 Zurich, Switzerland<br>Tel. +41-44-6355559<br>Email: <a href="mailto:r.friedman@bioc.uzh.ch">r.friedman@bioc.uzh.ch</a><br>Skype: ran.friedman<br>
------------------------------------------------------<br><br>shahid nayeem wrote:<br>> Dear all<br>> What are the analysis tools which should be used on MD trajectory file<br>> in order to find potential aggregation sites of a protein. Anyone can<br>
> tell me about specific resource material on use of Gromacs to predict<br>> protein aggregation hot spots from MD trajectory anlysis.<br>> Shahid Nayeem<br><br>--<br>gmx-users mailing list <a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br>
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</blockquote></div><br>