Docking
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
- 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
Bioinformatics Programming
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…)
Docking
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…)
Docking
[Tutorial] How to perform docking of zinc metalloproteins using Autodock Vina?
![[Tutorial] How to perform docking of zinc metalloproteins using Autodock Vina?](https://bioinformaticsreview.com/wp-content/uploads/2021/10/zn.jpg)
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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