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Docking

How to Find Binding Pocket/ Binding Site for Docking?

Dr. Muniba Faiza

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Finding binding pocket in target protein

Finding binding sites/pockets in a target protein is one of the important steps in docking studies. It is relatively easier to find a binding pocket in the proteins whose resolved structures are available in PDB than that of the predicted structures. In this article, we will discuss the ways to know a binding pocket or a binding site in a target protein.

When you are trying to find or design a drug for a particular target, you need to know the binding site within the protein. That protein’s structure would either be available in PDB or you would predict one. In both cases, you need to follow some protocol to find out the binding pocket else you can go for blind docking which is not considered as accurate as site-specific docking.

Case-I Finding binding pocket/site in the resolved structure of target protein

For the target protein whose structure is available in PDB, look for the associated literature on the same PDB entry page. This paper consists of all structural details explored during structure determination. You can find all binding or catalytic residues, important domains, and subunits of the target protein that you need to focus on before docking. Visualize the protein structure in a viewer such as Pymol and try to locate those binding residues. That’s how you can visualize the binding pocket in the protein with a known structure.

Case-II Finding binding pocket/site in the predicted structure of target protein

After you get the predicted structure of the target protein, you will have to predict binding pockets as well. For that, you can use an online server such as the CASTp server (http://sts.bioe.uic.edu/castp/). It provides quite accurate results in less time. It will also display the pocket in the visualizer. Note down those residues and visualize them in Pymol to locate them onto the structure. You can visualize a binding pocket on the surface of the target protein.

It is worth noting that the binding pocket may fall on more than one chain. In that case, you will have to keep both chains for docking and further simulation studies.

Dr. Muniba is a Bioinformatician based in New Delhi, India. She has completed her PhD in Bioinformatics from South China University of Technology, Guangzhou, China. She has cutting edge knowledge of bioinformatics tools, algorithms, and drug designing. When she is not reading she is found enjoying with the family. Know more about Muniba

Docking

[Tutorial] Performing docking using DockingPie plugin in PyMOL.

Dr. Muniba Faiza

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[Tutorial] Performing docking using DockingPie plugin in PyMOL.

DockingPie [1] is a PyMOL plugin to perform computational docking within PyMOL [2]. In this article, we will perform simple docking using DockingPie1.2.

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Docking

How to install the DockingPie plugin on PyMOL?

Dr. Muniba Faiza

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How to install DockingPie plugin on PyMOL?

DockingPie [1] is a plugin of PyMOL [2] 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).

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Docking

[Tutorial] Installing Pyrx on Windows.

Dr. Muniba Faiza

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[Tutorial] Installing Pyrx on Windows.

Pyrx [1] is another virtual screening software that also offers to perform docking using Autodock Vina. In this article, we will install Pyrx on Windows. (more…)

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Docking

How to install Autodock4 on Ubuntu?

Dr. Muniba Faiza

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How to install Autodock4 on Ubuntu?

Autodock suite is used for docking small molecules [1]. Recently, Autodock-GPU [2] is developed to accelerate the docking process. Its installation is described in this article. In this tutorial, we will install Autodock 4.2.6 on Ubuntu.

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Docking

What values are considered as good or bad in computational docking?

Dr. Muniba Faiza

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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 this in detail. (more…)

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Bioinformatics Programming

How to sort binding affinities based on a cutoff using vs_analysis.py script?

Dr. Muniba Faiza

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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…)

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Docking

Virtual Screening using Autodock Vina: Frequently Asked Questions & Answers for Starters

Dr. Muniba Faiza

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Virtual Screening using Autodock Vina: Virtual Screening: 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…)

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Docking

[Tutorial] How to perform docking of zinc metalloproteins using Autodock Vina?

Dr. Muniba Faiza

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[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 [1]. (more…)

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Docking

How to generate config file for docking using Autodock Tools?

Dr. Muniba Faiza

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How to generate config file for docking using Autodock Tools?

A configuration file is one of the required files for docking using Autodock Vina. In this article, we are going to generate a config file using Autodock Tools GUI [1]. (more…)

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Docking

How to install Autodock on Ubuntu (Linux) with CUDA GPU support?

Dr. Muniba Faiza

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How to install Autodock on Ubuntu (Linux) with CUDA GPU support?

Autodock [1] is most widely used for docking. To accelerate the docking process, especially, during virtual screening, Autodock-GPU [2] provides great help. In this article, we are going to install Autodock-GPU on Ubuntu. (more…)

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Docking

Autodock Vina: Uses & Applications

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Autodock Vina: Uses & Applications

Autodock Vina [1] 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…)

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Docking

How to perform virtual screening using Pyrx?

Dr. Muniba Faiza

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How to perform virtual screening using Pyrx?

Pyrx is a bioinformatics tool to perform virtual screening [1]. We previously provided an article on performing simple protein-ligand site-specific docking using Pyrx. In this article, we are going to perform virtual screening using Pyrx. (more…)

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Docking

How to perform metal ion-protein docking using idock?

Dr. Muniba Faiza

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How to perform metal ion-protein docking using idock?

Previously, we provided a tutorial on the installation of idock on Ubuntu (Linux). In this article, we are going to demonstrate the docking of a metal ion (such as Zn, Mg, Fe, etc.,) with a protein using idock. (more…)

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Docking

How to install idock on Ubuntu?

Dr. Muniba Faiza

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How to install idock on Ubuntu?

idock [1] 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…)

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Docking

How to analyze HADDOCK results using Pymol script generated from PRODIGY?

Dr. Muniba Faiza

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How to analyze HADDOCK results using Pymol script generated from PRODIGY?

In one of our previously published articles, we demonstrated protein-protein docking using HADDOCK2.4 [1]. In this article, we are going to demonstrate the HADDOCK results analysis using a Pymol script generated from the PRODIGY server [2]. (more…)

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Docking

Installing PatchDock on Ubuntu (Linux)

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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…)

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Docking

Protein-protein docking using HADDOCK2.4 web server

Dr. Muniba Faiza

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Protein-protein docking using HADDOCK2.4 web server

HADDOCK2.4 web server (https://bianca.science.uu.nl/haddock2.4/) [1] 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…)

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Docking

How to perform site-specific docking using Pyrx?

Dr. Muniba Faiza

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How to perform site-specific docking using Pyrx?

Pyrx [1] is a virtual screening software that allows the docking of multiple ligands with a target protein. Previously, we provided an article on the installation of Pyrx in Ubuntu. In this article, we are going to perform protein-ligand docking using Pyrx. (more…)

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Software

How to install sdsorter on Ubuntu (Linux)?

Dr. Muniba Faiza

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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…)

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Docking

Video Tutorial: How to use vs_analysis Python script for virtual screening result analysis of Autodock Vina?

Dr. Muniba Faiza

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How to use vs_analysis python script for virtual screening result analysis of Autodock Vina

This is a demonstration video of our previously mentioned Python script (vs_analysis.py) for virtual screening results analysis of Autodock Vina. (more…)

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