MCS alignment with rdkit and pymol #chemoinformatics #pymol #RDKit

Molecular alignment is very important procedure for drug design. There are lots of way to align molecules. RDKit has lots of function to align molecules.

https://www.rdkit.org/docs/source/rdkit.Chem.rdMolAlign.html

I often use Open3DALIGN or other similar methods. And recently I found another useful alignment tool for pymol named ‘mcsalign’.

If reader has already installed pymol, you can use mcsalign after installing following packages.

$ mamba install -c schrodinger pymol-psico
$ mamba install -c rdkit rdkit
$ mamba install -c speleo3 csb

Mcsaling is implemented in psico package and it uses rdkit rdFMCS for finding MCS.

To use mcsalign, user need to import psico.mcsalign in pymol. After importing the psico.mcsalign, main two commands will be available. One is mcsalign which aligns a molecule to template molecule and extra_fit which aligns set of molecules to template molecule.

I uploaded example code about MCSALIGN. For convenience, I controled pymol from jupyter-notebook with rdkit. I launched pymol as server mode before running the code. Pymol can launch serve mode with -R option.

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As you can see, mcsalign can align molecules based MCS. And extra_fit can align set of molecules against template molecule. It will be useful tool for structural alignment n many cases.

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Published by iwatobipen

I'm medicinal chemist in mid size of pharmaceutical company. I love chemoinfo, cording, organic synthesis, my family.

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