Hello,
I use RDKit to embed initial conformations for docking. The issue is
with saturated rings. I can use a single random conformer but its
geometry may be unsuitable and the whole molecule will fail to dock. I
can use several starting conformers for docking and to avoid docking of
very similar conformers I can select a few diverse conformers based on
RMSD between rings only. However, the issue occurs if a molecule has
several such saturated rings. The current workaround is to compute RMSD
between corresponding rings individually, then average RMSD values and
select a diverse set of conformers. It may work to some extend.
However I'm curious whether a better solution possible? Can we sample
rings individually and embed a molecule using pre-generated conformers
of some parts (rings)? I know about the restricted conformer enumeration
function, but it will work if we supply only a single connected part as
fixed. It should not work if we have two disconnected parts (rings) with
3D coordinates, because we do not know their relative position to
generate 3D coordinates for the rest of atoms in a molecule.
Maybe someone will have some ideas/suggestions?
Kind regards,
Pavel
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