In this article. we are creating a pie chart of the docking score of five different compounds docked with the same protein.
With the new year, we are going to start with a very simple yet complicated topic (for beginners) in bioinformatics. In this tutorial, we provide a...
Previously, we provided a similar script to download ligand SMILES from PDB ligand IDs. In this article, we are downloading PDB ligand structures from their corresponding...
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...
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...
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...
In this article, we provide a simple Python script to download files from an FTP server using Python.
VMD allows converting PDB to PSF format but sometimes it gives multiple errors. Therefore, in this article, we are going to convert PDB into PSF format...
As mentioned in some of our previous articles, RDKit provides a wide range of functions. In this article, we are using RDKit [1] to draw a...
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...
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.
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...
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...
Previously, we have provided a tutorial on using dssp_parser to extract all helices including long and short separately. Now, we have provided a new python script...
The x, y, and z coordinates of atoms are provided in the PDB file. One way to extract them is by using the Biopython package [1]....
A new Python package named ‘dssp_parser‘ is developed to parse DSSP files. This package fetches all helices including long and short ones from DSSP files.
Here is a Python script that helps you calculate the center of mass of a protein using the Pymol [1].
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