QSAR - Anonymous questions

Dear friends and members of our Society,

my proposal to all of you is not to react to questions which
are sent by people who just present their name and a
personal e-mail address but not the name of their
institution (see the e-mail below, which was sent to the
list just recently).

Best regards

Hugo

 
Prof. Dr. Hugo Kubinyi, Donnersbergstrasse 9
D-67256 Weisenheim am Sand, Germany
FAX +49-6353-508233, E-mail kubinyi#,#t-online.de
HomePage http://home.t-online.de/home/kubinyi

"Guosheng Wu" <wu_guosheng2002|-|yahoo.com> wrote:
> ---
>
> Hello everyone,
>
> I wonder if anyone has done detailed analysis of force field
> on the performance of protein-ligand docking?
>
> It seems that the Class I force field (CHARMM, AMBER,...) were
> parameterized for protein and DNA systems, while the Class II
> force field(MM3, MMFF94, CFF95...)is best for small organic
> molecules.
>
> The issue comes when one is interested in protein-ligand docking:
> what kinds of potentials and parameters should be used for
> inter-molecular interactions(energies & forces)?
>
> Maybe most studies simply use the force field of Class I, but
> will that bring significant error to the docking results?
>
> I heard there has been progress on more "generalized" force field
> which is supposed to fit both big and small molecules.
>
> I wonder if there has any systematical study on the effect of force field
> (class I, II, mixed, or "generalized") on the final docking results.
> Maybe this error can be smaller than errors from other kinds of approximations,
> such as limitation of sampling, so not a big deal?
>
> Hope to get some perspectives from the list, and thanks a lot in advance.
>
> Sincerely,
>
> Guosheng Wu
>
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Received on 2003-06-17 - 07:01 GMT