QSAR - Force field for protein-ligand docking

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 2003-06-14 - 22:36 GMT