DockingAnalyzer.py: A New Python script to Identify Ligand Binding in Protein Pockets.
High-throughput virtual screening (HTVS) is a pivotal technique in drug discovery that…
How to copy and rename files simultaneously in same directory in Ubuntu (Linux)?
Copying and renaming files from one destination to another is easily accomplished…
Free_Energy_Landscape-MD: Python package to create Free Energy Landscape using PCA from GROMACS.
In molecular dynamics (MD) simulations, a free energy landscape (FEL) serves as…
VS_Analysis: A Python package to perform post-virtual screening analysis
Virtual screening (VS) is a crucial aspect of bioinformatics. As you may…
vs_interaction_analysis.py: Python script to perform post-virtual screening analysis
Analyzing the results of virtual screening (VS) performed with Autodock Vina can…
How to obtain ligand structures in PDB format from PDB ligand IDs?
Previously, we provided a similar script to download ligand SMILES from PDB…
How to obtain SMILES of ligands using PDB ligand IDs?
Fetching SMILE strings for a given number of SDF files of chemical…
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…
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)…
How to download files from an FTP server using Python?
In this article, we provide a simple Python script to download files…
How to convert the PDB file to PSF format?
VMD allows converting PDB to PSF format but sometimes it gives multiple…
smitostr.py: Python script to convert SMILES to structures.
As mentioned in some of our previous articles, RDKit provides a wide…
How to preprocess data for clustering in MATLAB?
Data preprocessing is a foremost and essential step in clustering based on…
How to calculate drug-likeness using RDKit?
RDKit allows performing multiple functions on chemical compounds. One is the quantitative…
sdftosmi.py: Convert multiple ligands/compounds in SDF format to SMILES.
You can obtain SMILES of multiple compounds or ligands in an SDF…
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…
tanimoto_similarities.py: A Python script to calculate Tanimoto similarities of multiple compounds using RDKit.
RDKit is a very nice cheminformatics software. It allows us to perform…
How to commit changes to GitHub repository using vs code?
In this article, we are providing a few commands that are used…
