ADL: Theory in Vina tutorial video?

mcmartin at student.matnat.uio.no mcmartin at student.matnat.uio.no
Thu Apr 16 01:31:48 PDT 2009


Hi all,

So I'm watching the vina tutorial video and I got a little puzzled with the
theory explanation. They say:

"It is often said that the global minimum corresponds to the native
conformation, however this is not correct, a deeper but narrower peak may
actually be less preferable, because of entropy"

Oleg says this while pointing at the conformation of lowest energy,
which as I have understood, is the "strongest" binding energy. There are a
couple of things in this sentence that I do not understand and I hope you
can help me out:

1. Why does he talk about a ligand-receptor complex with a "native"
conformation? I thought the term native conformation was strictly applied to
proteins with the proper functional folding?

2. So I understand in the in silico experiment entropy is lost upon
ligand-receptor binding,  especially since AutoDock neglects the solvent
molecules (Unless the entropy of the desolvation state is taken into account
with the AMBER force fields, which is not yet clear to me, even though I
have read Cornell et al. 1995) So why is a _wider_ peak more preferable in
terms of entropy? In other words, what does the width of the peak
represent?

I hope you can help me out!

Marcus Martinez



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