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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

How to obtain SMILES of ligands using PDB ligand IDs?

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How to obtain SMILES of ligands using PDB ligand IDs?

Fetching SMILE strings for a given number of SDF files of chemical compounds is not such a trivial task. We can quickly obtain them using RDKit or OpenBabel. But what if you don’t have SDF files of ligands in the first place? All you have is Ligand IDs from PDB. If they are a few then you can think of downloading SDF files manually but still, it seems time-consuming, especially when you have multiple compounds to work with. Therefore, we provide a Python script that will read all Ligand IDs and fetch their SDF files, and will finally convert them into SMILE strings. (more…)

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Bioinformatics Programming

How to get secondary structure of multiple PDB files using DSSP in Python?

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How to get secondary structure of multiple PDB files using DSSP in Python?

In this article, we will obtain the secondary structure of multiple PDB files present in a directory using DSSP [1]. You need to have DSSP installed on your system. (more…)

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Bioinformatics Programming

vs_analysis_compound.py: Python script to search for binding affinities based on compound names.

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vs_analysis_compound.py: Python script to search for binding affinities based on compound names.

Previously, we have provided the vs_analysis.py script to analyze virtual screening (VS) results obtained from Autodock Vina. In this article, we have provided another script to search for binding affinity associated with a compound. (more…)

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