AMBER Archive (2004)

Subject: Re: AMBER: protein-protein interaction

From: David A. Case (
Date: Wed Mar 17 2004 - 10:37:40 CST

On Wed, Mar 17, 2004, Oscar Rey i Puiggrs wrote:
> I'm trying to measure the energy of protein-protein interaction, and the
> effect of mutating some essential residues. I've noticed that MM-PBSA is a
> common strategy in order to measure ligand-receptor interaction energy. Is
> it a good strategy to measure protein-protein interaction energy by means of
> this technique? If not, could anybody point me to a good strategy?

Protein-protein interaction energies can be quite tricky with MM-PBSA. You
might want to look at our recent paper on this:

%A H. Gohlke
%A D.A. Case
%T Converging Free Energy Estimates: MM-PB(GB)SA Studies on the
Protein-Protein Complex Ras-Raf
%J J. Comput. Chem.
%V 25
%P 238-250
%D 2004

...hope this helps...dac


================================================================== David A. Case | e-mail: Dept. of Molecular Biology, TPC15 | fax: +1-858-784-8896 The Scripps Research Institute | phone: +1-858-784-9768 10550 N. Torrey Pines Rd. | home page: La Jolla CA 92037 USA | ================================================================== ----------------------------------------------------------------------- The AMBER Mail Reflector To post, send mail to To unsubscribe, send "unsubscribe amber" to