ADL: parameter optimization of vina scoring function

meginir urestal meginir.urestal at gmail.com
Thu Jan 16 02:40:57 PST 2014


Hello all,
I'm currently docking a series of nucleotides in a certain protein using
Vina. In order to enhance the results (number of good poses -compared to a
crystal structure- and their relative positions in a given docking result)
I'm currently tweaking the scoring function through the hydrogen bond
weight parameter.
Using the same protein and ligand, I realized several docking runs with
everything identical except for the hbond weight (and using the same random
seed for comparability). I then compared the results between these
different runs. However, I'm having trouble getting something out of this
modus operandi. In fact several questions have come up while considering
this:

      - is parameter optimization a useful thing to do?
      - Is this a good way to optimize parameters?
      - is parameter optimization valid only for the ligand it has been
done for, or can it be extrapolated to a family of similar ligands or
perhaps all ligands for a given receptor? A priori, the answer is no, but
I'd like a different opinion.
      - Is parameter optimization in the way that I perceive it (changing
only one parameter at a time) any good considering that a scoring function/
energy function is multidimentional?

Thanks,
meginir


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