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Bioinformatics Programming

How to calculate drug-likeness using RDKit?

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How to calculate drug-likeness using RDKit?

RDKit [1] allows performing multiple functions on chemical compounds. One is the quantitative estimation of drug-likeness also known as QED properties. These properties include molecular weight (MW), octanol-water partition coefficient (ALOGP), number of hydrogen bond donors (HBD), number of hydrogen bond acceptors (HBA), polar surface area (PSA), number of rotatable bonds (ROTB), number of aromatic rings (AROM), structural alerts (ALERTS).

In this article, we provide a short Python script to help you calculate all the above-mentioned molecular descriptors.

#######################################################
#!/usr/bin/env python3

import os
import sys
from rdkit import Chem
from rdkit.Chem import QED

file_name = sys.argv[1]
sppl = Chem.SDMolSupplier(file_name) #we are using sdf file of compounds here

for mol in sppl:
    print( QED.properties( mol ) )
#######################################################

Save this script, for example as qed_properties.py and you can run it as:
$ python3 qed_properties.py ligands.sdf
Ligands.sdf is the compound sdf file.


References

1. RDKit: Open-Source Cheminformatics Software (RRID:SCR_014274)

Dr. Muniba is a Bioinformatician based in New Delhi, India. She has completed her PhD in Bioinformatics from South China University of Technology, Guangzhou, China. She has cutting edge knowledge of bioinformatics tools, algorithms, and drug designing. When she is not reading she is found enjoying with the family. Know more about Muniba

Bioinformatics Programming

sdftosmi.py: Convert multiple ligands/compounds in SDF format to SMILES?

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sdftosmi.py: Convert multiple ligands/compounds in SDF format to SMILES?

You can obtain SMILES of multiple compounds or ligands in an SDF file in one go. Here, we provide a simple Python script to do that. (more…)

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Bioinformatics Programming

tanimoto_similarities_one_vs_all.py – Python script to calculate Tanimoto Similarities of multiple compounds

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tanimoto_similarities_one_vs_all.py – Python script to calculate Tanimoto Similarities of a compound with multiple compounds

We previously provided a Python script to calculate the Tanimoto similarities of multiple compounds against each other. In this article, we are providing another Python script to calculate the Tanimoto similarities of one compound with multiple compounds. (more…)

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Bioinformatics Programming

tanimoto_similarities.py: A Python script to calculate Tanimoto similarities of multiple compounds using RDKit.

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tanimoto_similarities.py: A Python script to calculate Tanimoto similarities of multiple compounds using RDKit.

RDKit [1] is a very nice cheminformatics software. It allows us to perform a wide range of operations on chemical compounds/ ligands. We have provided a Python script to perform fingerprinting using Tanimoto similarity on multiple compounds using RDKit. (more…)

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