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  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.
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.
- 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.
How to install Autodock4 on Ubuntu?
Autodock suite is used for docking small molecules . Recently, Autodock-GPU  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.
What values are considered as good or bad in computational docking?
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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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?
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 . (more…)
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?
Pyrx is a bioinformatics tool to perform virtual screening . 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…)
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?
In one of our previously published articles, we demonstrated protein-protein docking using HADDOCK2.4 . In this article, we are going to demonstrate the HADDOCK results analysis using a Pymol script generated from the PRODIGY server . (more…)
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?
Pyrx  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…)
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…)
Video Tutorial: 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…)
Basic Methodology to Predict Antigen-Antibody Interactions in silico
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What is Virtual Screening in Bioinformatics?
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. (more…)
Blind Docking vs Site-specific Docking
We have provided several tutorials on docking including both types: blind docking & site-specific docking using Autodock Vina. In this article, we are going to compare both methods of docking. (more…)
Most widely used software for docking results image generation
Computational docking is an important technique in bioinformatics. The docking result interpretation and representation are important as well. There are various software available for docking result analysis and offer to generate high-quality images for publications. In this article, we will mention such a few software for the same purpose. (more…)
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