Dear all,

I want to align 250 compounds that binding to the same pocket to one of the
9 available crystal ligands. I chose the reference ligand based on the
Morgan2 similarity to the probe molecule. Then I align the 2 compounds

pyO3A = rdMolAlign.GetO3A(qmol, refmol, prbCid=qconfID, refCid=0,
RMSD = pyO3A.Align()

​and keep only the conformer of the probe with the lowest RMSD to the
reference compound. However, the alignment looks terrible when I visualize
it, so I would like to ask if there is any way to align the maximum common
substructure only. I tried to align only the core of both molecules as
defined by MurckoScaffold.GetScaffoldForMol(mol)​, but still the alignment
looks bad. I have seen in the documentation how to find the maximum common
substructure with rdFMCS.FindMCS but before I engage into programming it I
would like to know if there is any automatic way to find it on the fly
while aligning the 2 molecules.



Thomas Evangelidis

Research Specialist
CEITEC - Central European Institute of Technology
Masaryk University
Kamenice 5/A35/1S081,
62500 Brno, Czech Republic


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