If you are a beginner in the field of bioinformatics, you must have heard of the term “virtual screening” (VS). In this article, we will discuss the basic meaning of VS and its significance in bioinformatics.
The VS is one of the important techniques in bioinformatics that is used during the drug designing process. In this technique, we try to identify best-fit compounds/molecules/ligands that are most likely to bind to a receptor, i.e., our target protein. The target protein consists of some pockets within its structure. Amongst which there is a binding pocket for such ligands.
The ligands are available in a database such as Pubchem, Drugbank, ZINC, and many more. The ligands could be of any nature including natural compounds, metabolites, FDA-approved drugs, etc. It completely depends upon your study whether you are looking for a natural inhibitor or an FDA-approved drug.
How do we perform VS?
A detailed stepwise basic methodology is explained in our previous article. Generally, after gathering all information about the binding pocket and binding residues in the receptor protein, you have to select and download a database of compounds/molecules/ligands for docking. These ligands are docked within the defined binding pocket of the target protein with the help of suitable software. The software helps to find out the ligands that can bind to the target protein efficiently. Basically, since we dock a large number of ligands with the protein, therefore, we select the best ligands first on the basis of the lowest binding affinity and then further on the basis of interactions with the binding residues. Ultimately, we have some ligands that show binding with the target protein. We further filter these ligands on the basis of other parameters such as ADMET properties. It is another important aspect of drug designing.
Software for VS
There is software available for VS including:
- GOLD (paid software)
- GLIDE (paid software)
- Autodock Vina (open access)
- Schrodinger (paid software)
You can find some tutorials on VS under the ‘Further Reading’ section.
[Tutorial] Performing docking using DockingPie plugin in PyMOL.
How to install the DockingPie plugin on PyMOL?
DockingPie  is a plugin of PyMOL  made to fulfill the purpose of docking within the PyMOL interface. This plugin will allow you to dock using four different algorithms, namely, Vina, RxDock, SMINA, and ADFR. It will also allow you to perform flexible docking. Though the installation procedure is the same for all OSs, in this article, we are installing this plugin on Ubuntu (Linux).
[Tutorial] Installing Pyrx on Windows.
How to install Autodock4 on Ubuntu?
What values are considered as good or bad in computational docking?
How to sort binding affinities based on a cutoff using vs_analysis.py script?
Previously, we have provided a Python script (vs_analysis.py) to analyze the virtual screening (VS) results of Autodock Vina. Now, we have updated this script to sort binding affinities based on user inputted cutoff value. (more…)
Virtual Screening using Autodock Vina: Frequently Asked Questions & Answers for Starters
Virtual Screening (VS) is one of the important techniques in bioinformatics. It can be easily performed using Autodock Vina. We have provided detailed articles on this topic. In this article, we are trying to answer some FAQs for beginners. (more…)
[Tutorial] How to perform docking of zinc metalloproteins using Autodock Vina?
Proteins containing zinc atoms are docked in a different way than that of the normal simple proteins. Zinc atoms must be considered by a force field during the docking process. In this article, we are going to dock zinc metalloprotein with a ligand using Autodock Vina . (more…)
How to generate config file for docking using Autodock Tools?
How to install Autodock on Ubuntu (Linux) with CUDA GPU support?
Autodock  is most widely used for docking. To accelerate the docking process, especially, during virtual screening, Autodock-GPU  provides great help. In this article, we are going to install Autodock-GPU on Ubuntu. (more…)
Autodock Vina: Uses & Applications
Autodock Vina  is one of the most widely used bioinformatics software for computational docking. For beginners and those who are new to the field of bioinformatics, such software may appear confusing without having an initial idea of what this software actually used for. In this article, we have discussed some of the primary uses and applications of Autodock Vina software. (more…)
How to perform virtual screening using Pyrx?
How to perform metal ion-protein docking using idock?
How to install idock on Ubuntu?
idock  is a multithreaded software based on Autodock Vina. It is a virtual screening tool for flexible ligand docking. It also supports 27 different chemical elements including zinc, magnesium, iron, calcium, etc. In this article, we are going to install idock on Ubuntu. (more…)
How to analyze HADDOCK results using Pymol script generated from PRODIGY?
Installing PatchDock on Ubuntu (Linux)
PatchDock is a docking algorithm that is based on the shape complementarity principle [1,2]. It performs molecular docking of any two types of molecules including proteins, DNA, drugs, and peptides. In this article, we are going to install PatchDock on Ubuntu (Linux). (more…)
Protein-protein docking using HADDOCK2.4 web server
HADDOCK2.4 web server (https://bianca.science.uu.nl/haddock2.4/)  is used for protein-protein docking and their modeling. Not only proteins, but it can also process peptides, small molecules, and nucleic acids. In this article, we are going to perform protein-protein docking. (more…)
How to perform site-specific docking using Pyrx?
How to install sdsorter on Ubuntu (Linux)?
sdsorter is a tool that helps in the easy manipulation of SDF files. It takes a single file as input and also provides a single output file. In this article, we are going to install sdsorter on Ubuntu (Linux). (more…)