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: [email protected] 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 > > > -- gmx-users mailing list [email protected] http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [email protected]. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
