[Rdkit-discuss] sampling of ring conformation for docking

[Pavel P. <pav...@uk...>]

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