[phenixbb] question about free energy calculation in protein complex

Ed Pozharski epozh001 at umaryland.edu
Fri May 14 04:17:42 PDT 2010

With all due respect to people behind PISA server (which is a fantastic
tool), there is probably no good answer to the crystallogrphy's
question.  The main contribution to the free energy of protein
association is probably hydrophobic interaction, while the mentioned
types of interactions are hard to quantify (salt bridges, for instance,
can be both stabilizing and destabilizing depending on their
environment).  Remember that most of these specific interactions are
substituted by corresponding interactions with solvent upon complex
dissociation.  There are couple of servers you can try (and plenty of
literature on the subject).


Also remember that crystal structures do not always contain all the
information needed for accurate estimates of free energies.  And maybe
consider a different alias :)


On Thu, 2010-05-13 at 17:16 -0600, Maia Cherney wrote:
> PISA server
> crystallogrphy wrote:
> > Hi,
> > I am trying to calculate the free energy of association for structure 
> > of a protein complexes based on the salt bridges, H-bonds and van der 
> > waals interaction?  Does any one know how to do it?
> >
> > Thanks!
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Edwin Pozharski, PhD, Assistant Professor
University of Maryland, Baltimore
When the Way is forgotten duty and justice appear;
Then knowledge and wisdom are born along with hypocrisy.
When harmonious relationships dissolve then respect and devotion arise;
When a nation falls to chaos then loyalty and patriotism are born.
------------------------------   / Lao Tse /

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