While doing molecular dynamics (MD) simulation, it can be difficult to calculate the number of steps or nsteps for an MD run accurately. In this article,...
Detecting viruses and bacteria in RNA-seq data with less false positive rate is a difficult task. A new tool is introduced to detect pathogens in RNA-seq...
In this article. we are creating a pie chart of the docking score of five different compounds docked with the same protein.
AlphaFold is a popular artificial intelligence based protein prediction tool [1]. Though it predicts good protein structures, it lacks the capability to predict the small molecules...
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...
Due to the advancement of machine learning (ML) methods, we can find increasing applications of them in the field of bioinformatics as well. ML is being...
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...
After performing computational docking, a question that comes to mind most is “what docking score is considered good or bad”. In this article, we will discuss...
Previously, we provided a tutorial for PyVol plugin [1] installation. In this article, we will calculate the binding pocket volume of protein using the same plugin...
Electron density maps are available for most of the protein structures in PDB. Therefore, in this article, we are using PDB to generate electron density maps...
Previously, we provided a Python script to download data over an FTP server. This article will use the Linux command to download multiple directories and subdirectories...
Openbabel [1] offers a wide range of operations. One of which is file format conversion which is most widely used. In this article, we will describe...
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...
Data preprocessing is a foremost and essential step in clustering based on machine learning methods. It removes noise and provides better results. In this article, we...
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...
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