I would like to align two molecules using the following nodes for each molecules: RDKit Add Hs => RDkit add Conformers => Rdkit Optimize Geometry => RDkit Remove Hs. Then for the reference compound, I select the 3D structure with the minimal energy from Rdkit Optimize Geometry and do a RDKit open 3D alignment. When I look into the result of the best score from RDKit open 3D alignement, I have the feeling that this could be optimized.
Is this approach appropriate for alignment of compounds to a reference compound? What would be the best method to select the best alignment? Could I use the best score result from the RDKit open 3D alignment?
Then I am wondering if the parameter could be fine tune to improve the workflow:
- For Rdkit Optimize Geometry, what would be your recommendation for Number of conformers (I put 200), Maximum number of tries to generate conformers (30) and RMS threshold for keeping a conformer (0.5). I use respectively 200, 30 and 0.5.
- How many iterations for Rdkit Optimize Geometry Iterations (I kept 1000 and I did not tick to remove starting coordinates before optimizing the molecule).
- For RDKit open 3D alignement, how many Maximal number of iterations? I use 200.
Thanks for your help,