Bioinformatics Programming
Some common awk bash commands to modify multi-FASTA files

Bioinformatics Programming
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
Bioinformatics Programming
How to make swarm boxplot?

With the new year, we are going to start with a very simple yet complicated topic (for beginners) in
Bioinformatics Programming
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
Bioinformatics Programming
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
Bioinformatics Programming
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
Bioinformatics Programming
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
Bioinformatics Programming
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
Bioinformatics Programming
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
Bioinformatics Programming
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
Bioinformatics Programming
How to preprocess data for clustering in MATLAB?

Data preprocessing is a foremost and essential step in clustering based on machine learning methods.
Bioinformatics Programming
How to calculate drug-likeness using RDKit?

RDKit [1] allows performing multiple functions on chemical compounds. One is the quantitative estima
Bioinformatics Programming
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
Bioinformatics Programming
tanimoto_similarities_one_vs_all.py – Python script to calculate Tanimoto Similarities of multiple compounds

We previously provided a Python script to calculate the Tanimoto similarities of multiple compounds
Bioinformatics Programming
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
Bioinformatics Programming
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
Bioinformatics Programming
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
Bioinformatics Programming
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
Bioinformatics Programming
dssp_parser: A new Python package to extract helices from DSSP files.

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