[gmx-users] FEP method in protein-ligand systems

[Diego Nolasco]

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 <dmobley at gmail.com>:
>
> 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
> >
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