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

David Mobley dmobley at gmail.com
Fri Jul 27 05:47:09 CEST 2007


> 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.


> Thanks a lot,
> Diego Nolasco
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