Subject: General scoring functions for PP, PL, and LL

From: Guosheng Wu <wu_guosheng2002=at=yahoo.com>
Date: Wed, 1 Sep 2004 08:30:25 -0700 (PDT)

Hi there,

In the computation of protein(P)-ligand(L) binding
free energy, one would like to have a quick and
accurate scoring function to evaluate all of those
non-bond interactions between atomic pairs of PP, PL,
and LL, for the strain energy of the target, binding
energy, and strain energy for ligand, respectively. So
that a more reasonable comparison with the
experimental activities can be justified.

However, things are often very complicated. It seems
most of current scoring functions are focused on the
PL part. For the LL part, simple energy difference
(between the solution state & binding state) from MM
is often claimed to be good enough. For the PP part,
it may be more difficult to quantify and validate, or
it simply adds more noise rather than useful
information. One may argue that the PL part is usually
the dominant component. Still it's not that simple in
many cases, otherwise, no one would really care about
the business of flexibility.

Does anyone notice any kind of "general" approach for
this task? Physically, should there be much difference
for these three kinds of potentials?

I would like to get your comments or reminding of
relevant literature. 

Thanks a lot. 

Guosheng

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