An experiment with MorganFP #RDKit #chemoinformatics

Tokyo Olympic opening ceremony is coming. I hope the Olympic will be safe and secure.

Today I tested to compare fingerprints from molecule and fragments. Because if I can construct the identical fingerprint from fragments, it’s useful.

Following code is very simple example used 1,3 and 1,2 di-substituted benzene.

I calculated fingerprint of each molecule and calculated fingerprints. The result shows that tanimoto similarity of mol1 and mol2 was quite low but mol3 and mol4 is 1.0.

It indicates that fingerprint from fragments can’t consider location where the substituents are.

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view raw fp_calc.ipynb hosted with ❤ by GitHub

This is very simple example of fingerprint from fragments. But it’s worth for me to know the behavior of fragment fingerprint.


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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