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 to find the first and last residue in each helix file.
You can extract these residues using the “start_end_helix_res.py” file. This file is provided in the package. Download the dssp_parser package from our GitHub account.
The input files are long helices files that are obtained from parsing the initial dssp files of PDB structures. The output is a CSV file containing the helix name, start residue, and end residue of each file. Run the script as shown below:
$ python3 start_end_helix_res.py
For more information on this package, visit the following link:
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. (more…)
How to obtain ligand structures in PDB format from PDB ligand IDs?
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 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…)