Re: [gmx-users] FEP method in protein-ligand systems
Thank you David, I really appreciated your help. I will read your paper and try to go on. Thank you very much! 2007/7/27, David Mobley <[EMAIL PROTECTED]>: > > Hi, > > > I am trying to run some simulations in attempts to calculate binding > free > > energy between ligands and a protein using the FEP method, but until now > I > > did not have any success. I have been looking for bibliography over this > > subject, but, as you may know, there aren't many works about FEP. What I > > found is one job where the solvation of amino acids analogs was > calculated, > > but there wasn't any mention about the usage of the method in > protein-ligand > > systems. What I would like to ask is: Is it possible to develop work > over > > free energy calculations using the FEP method in protein-ligand systems? > > You might start with my recent JMB paper for references. > http://dx.doi.org/10.1016/j.jmb.2007.06.002. There are also recent > reviews of free energy calculations by Rodinger and Pomes, and by > David Kofke, as well as one by Michael Shirts, myself, and John > Chodera that will be out in Annual Reports in Computational Chemistry > that will be out soon. > > For that matter, any literature search on "free energy perturbation" > should turn up lots of hits. I get 2,600 in a Google scholar search on > the subject ( > http://scholar.google.com/scholar?hl=en&lr=&q=%22free+energy+perturbation%22&btnG=Search > ). > Lots of hits for alchemical free energy calculations and thermodynamic > integration as well. I'm not sure why you think there aren't many > publications on FEP. > > David > > > > Thanks a lot, > > Diego Nolasco > > > > ___ > > gmx-users mailing listgmx-users@gromacs.org > > http://www.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 > > > ___ > gmx-users mailing listgmx-users@gromacs.org > http://www.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 > ___ gmx-users mailing listgmx-users@gromacs.org http://www.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
Re: [gmx-users] FEP method in protein-ligand systems
Hi, > I am trying to run some simulations in attempts to calculate binding free > energy between ligands and a protein using the FEP method, but until now I > did not have any success. I have been looking for bibliography over this > subject, but, as you may know, there aren't many works about FEP. What I > found is one job where the solvation of amino acids analogs was calculated, > but there wasn't any mention about the usage of the method in protein-ligand > systems. What I would like to ask is: Is it possible to develop work over > free energy calculations using the FEP method in protein-ligand systems? You might start with my recent JMB paper for references. http://dx.doi.org/10.1016/j.jmb.2007.06.002. There are also recent reviews of free energy calculations by Rodinger and Pomes, and by David Kofke, as well as one by Michael Shirts, myself, and John Chodera that will be out in Annual Reports in Computational Chemistry that will be out soon. For that matter, any literature search on "free energy perturbation" should turn up lots of hits. I get 2,600 in a Google scholar search on the subject (http://scholar.google.com/scholar?hl=en&lr=&q=%22free+energy+perturbation%22&btnG=Search). Lots of hits for alchemical free energy calculations and thermodynamic integration as well. I'm not sure why you think there aren't many publications on FEP. David > Thanks a lot, > Diego Nolasco > > ___ > gmx-users mailing listgmx-users@gromacs.org > http://www.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 > ___ gmx-users mailing listgmx-users@gromacs.org http://www.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
[gmx-users] FEP method in protein-ligand systems
Hello there, I am trying to run some simulations in attempts to calculate binding free energy between ligands and a protein using the FEP method, but until now I did not have any success. I have been looking for bibliography over this subject, but, as you may know, there aren't many works about FEP. What I found is one job where the solvation of amino acids analogs was calculated, but there wasn't any mention about the usage of the method in protein-ligand systems. What I would like to ask is: Is it possible to develop work over free energy calculations using the FEP method in protein-ligand systems? Thanks a lot, Diego Nolasco ___ gmx-users mailing listgmx-users@gromacs.org http://www.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
