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. In this tutorial, we provide a simple code to plot swarm boxplot using matplotlib and seaborn.
Here, we provide a simple Python script to plot the docking score of a few protein complexes. The complex names, docking scores, and ligand types are provided in a CSV sheet. We are plotting the docking score of ligands on a box plot showing types of ligands in different colors.
Availability
The script is available on GitHub under the package ‘cheminformatics‘.
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 IDs. (more…)
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…)
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 using DSSP [1]. You need to have DSSP installed on your system. (more…)
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