[gmx-users] LIE method

[osmair oliveira]

Hi Tatiana,
If you just want to estimate the binding energy, I suggest that, 
initially, you use docking methodologies. For example, you can 
use AutoDock program, that is a free program.

I hope this help

Osmair
Brazil

> Date: Fri, 4 Dec 2009 09:25:56 +0100
> From: r.friedman at bioc.uzh.ch
> To: gmx-users at gromacs.org
> Subject: Re: [gmx-users] LIE method
> 
> Dear Tatiana,
> In principle you can estimate binding free energy differences using LIE
> (or LIECE). Your success will depend on the protein and proper
> parameters. The best way is to try ligands with known binding energies
> at first. Check the relevant literature for details and parameters.
> Ran.
> 
> 
> -- 
> ------------------------------------------------------
> Ran Friedman
> Postdoctoral Fellow
> Computational Structural Biology Group (A. Caflisch)
> Department of Biochemistry
> University of Zurich
> Winterthurerstrasse 190
> CH-8057 Zurich, Switzerland
> Tel. +41-44-6355559
> Email: r.friedman at bioc.unizh.ch
> Skype: ran.friedman
> ------------------------------------------------------
> 
> 
> 
> Tatiana de Arruda Campos Brasil de Souza wrote:
> > Dear users, 
> >
> > I want to estimate the affinity of a protein to two diferent ligands and 
> > compare the results. Is the LIE the best method to do that? Does any one 
> > have a reference that this kind of analysis is performed or an example of 
> > mdp? 
> >
> > Best regards,
> >
> > Tatiana
> >
> >
> >   
> 
> -- 
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