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Hi Tatiana,<br>If you just want to estimate the binding energy, I suggest that, <br>initially, you use docking methodologies. For example, you can <br>use AutoDock program, that is a free program.<br><br>I hope this help<br><br>Osmair<br>Brazil<br><br>> Date: Fri, 4 Dec 2009 09:25:56 +0100<br>> From: r.friedman@bioc.uzh.ch<br>> To: gmx-users@gromacs.org<br>> Subject: Re: [gmx-users] LIE method<br>> <br>> Dear Tatiana,<br>> In principle you can estimate binding free energy differences using LIE<br>> (or LIECE). Your success will depend on the protein and proper<br>> parameters. The best way is to try ligands with known binding energies<br>> at first. Check the relevant literature for details and parameters.<br>> Ran.<br>> <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: r.friedman@bioc.unizh.ch<br>> Skype: ran.friedman<br>> ------------------------------------------------------<br>> <br>> <br>> <br>> Tatiana de Arruda Campos Brasil de Souza wrote:<br>> > Dear users, <br>> ><br>> > I want to estimate the affinity of a protein to two diferent ligands and <br>> > compare the results. Is the LIE the best method to do that? Does any one <br>> > have a reference that this kind of analysis is performed or an example of <br>> > mdp? <br>> ><br>> > Best regards,<br>> ><br>> > Tatiana<br>> ><br>> ><br>> > <br>> <br>> -- <br>> gmx-users mailing list gmx-users@gromacs.org<br>> http://lists.gromacs.org/mailman/listinfo/gmx-users<br>> Please search the archive at http://www.gromacs.org/search before posting!<br>> Please don't post (un)subscribe requests to the list. Use the <br>> www interface or send it to gmx-users-request@gromacs.org.<br>> Can't post? Read http://www.gromacs.org/mailing_lists/users.php<br> <br /><hr />Chegou Windows 7. Agora com exibição de redes sem fio. <a href='http://www.microsoft.com/brasil/windows7/default.html?WT.mc_id=1539' target='_new'>Conheça.</a></body>
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