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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.

idock [1] tool is based on Autodock Vina. It also requires input files of the receptor and the ligand in PDBQT format.

Preparing protein & ligand

You have to prepare your protein and ligand of interest in pdbqt format. You can do it using Autodock tools. The procedure will remain the same. Define the pocket in the protein and save it as a PDBQT file. For more details, read this article for site-specific docking and this one for blind docking. All the steps are explained in these articles. Save the ligand in a directory.

Preparing configuration file

Prepare a configuration file for docking. Mention all coordinates of the grid box in this file and save it with an appropriate name. Here, we are saving it as ‘conf.txt‘. For more details on preparing configuration files, read the above-mentioned articles. Although configuration file is optional, you can pass all the coordinates and necessary information such as log file name, etc., in the command line as arguments. It is shown in the following section.

Performing docking

Open a terminal by pressing Ctrl+Alt+T and paste the following command:

$ idock --config conf.txt

Without the configuration file, run the following command:

$ idock --receptor protein.pdbqt --input_folder /path/to/ligand folder/zn --output_folder output --center_x 59.022 --center_y -38.123 --center_z 36.653 --size_x 40 --size_y 40 --size_z 40

It will take a few moments to finish docking depending upon the size of the protein.


References

  1. Li, H., Leung, K. S., & Wong, M. H. (2012, May). idock: A multithreaded virtual screening tool for flexible ligand docking. In 2012 IEEE Symposium on Computational Intelligence in Bioinformatics and Computational Biology (CIBCB) (pp. 77-84). IEEE.

Further Reading

How to install idock on Ubuntu?

Blind Docking vs Site-specific Docking

Protein-protein docking using HADDOCK2.4 web server

Where to find Docking and MD simulation software?

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

How to install idock on Ubuntu?

Dr. Muniba Faiza

Published

on

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)

Tariq Abdullah

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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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