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Bioinformatics Programming

Some common awk bash commands to modify multi-FASTA files

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awk commands for multi-FASTA files
Some basic operations on multi-FASTA sequence files is a tedious task without using bioinformatics p

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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 create a pie chart using Python?

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How to create a pie chart using Python?
In this article. we are creating a pie chart of the docking score of five different compounds docked

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Bioinformatics Programming

How to make swarm boxplot?

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How to make swarm boxplot?
With the new year, we are going to start with a very simple yet complicated topic (for beginners) in

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Bioinformatics Programming

How to obtain ligand structures in PDB format from PDB ligand IDs?

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How to obtain ligand structures in PDB format from PDB ligand IDs?
Previously, we provided a similar script to download ligand SMILES from PDB ligand IDs. In this arti

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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 t

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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

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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 obt

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Bioinformatics Programming

How to download files from an FTP server using Python?

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How to download files from an FTP server using Python?
In this article, we provide a simple Python script to download files from an FTP server using Python

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Bioinformatics Programming

How to convert the PDB file to PSF format?

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How to convert the PDB file to PSF format?
VMD allows converting PDB to PSF format but sometimes it gives multiple errors. Therefore, in this a

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Bioinformatics Programming

smitostr.py: Python script to convert SMILES to structures.

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smitostr.py: Python script to convert SMILES to structures.
As mentioned in some of our previous articles, RDKit provides a wide range of functions. In this art

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Bioinformatics Programming

How to preprocess data for clustering in MATLAB?

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How to preprocess data for clustering in MATLAB?
Data preprocessing is a foremost and essential step in clustering based on machine learning methods.

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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 estima

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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

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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

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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 operation

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Bioinformatics Programming

How to commit changes to GitHub repository using vs code?

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How to commit changes to GitHub repository using vs code?
In this article, we are providing a few commands that are used to commit changes to GitHub repositor

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Bioinformatics Programming

Extracting first and last residue from helix file in DSSP format.

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Extracting first and last residue from helix file in DSSP format.
Previously, we have provided a tutorial on using dssp_parser to extract all helices including long a

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Bioinformatics Programming

How to extract x,y,z coordinates of atoms from PDB file?

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How to extract x,y,z coordinates of atoms from PDB file?
The x, y, and z coordinates of atoms are provided in the PDB file. One way to extract them is by usi

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Bioinformatics Programming

dssp_parser: A new Python package to extract helices from DSSP files.

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A new Python package named ‘dssp_parser‘ is developed to parse DSSP files. This package

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Bioinformatics Programming

How to calculate center of mass of a protein structure using Python script?

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How to calculate center of mass of a protein structure using Python script?
Here is a Python script that helps you calculate the center of mass of a protein using the Pymol [1]

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Bioinformatics Programming

How to sort binding affinities based on a cutoff using vs_analysis.py script?

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How to sort binding affinities based on a cutoff using vs_analysis.py script?
Previously, we have provided a Python script (vs_analysis.py) to analyze the virtual screening (VS)

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