Docking
Raccoon2: A GUI facilitating virtual screenings with Autodock and Autodock Vina

In the previous article, a new plugin called ‘Raccoon’ was mentioned, which helps in preparing virtual screening using Autodock. It provides a simple graphical user interface (GUI) where you can easily load the ligand and protein files in Autodock and perform virtual screening. An advanced version of Raccoon called, ‘Raccoon2’ has been introduced by Forli et al., (2016) [1] as GUI to prepare and analyze Autodock and Autodock Vina virtual screenings.
Raccoon2 incorporates some new features such as an automatic server connection manager, loading multiple receptor structures and flexible residues, GUI for docking setup and grid box, result filtering options by energy or ligand efficiency, and interactions, easy management or remote jobs, and automatic installation of docking services (for Autodock Vina only).
How to install Raccoon2?
Raccoon2 is added in MGLTools and the installer can be downloaded from here. It is available for Windows, Linux, and MAC OS.
Once the installer is downloaded (let’s say in the Downloads directory), open the terminal and type the following commands:
$ cd Downloads
$ chmod +x mgltools_Linux-x86_64_1.5.7rc1_install
$ ./mgltools_Linux-x86_64_1.5.7rc1_install
If it shows an error “Permission denied”, then try
$ sudo ./mgltools_Linux-x86_64_1.5.7rc1_install
In case of a tar package, type the following commands in the terminal:
$ cd Downloads/
$ tar xvzf mgltools_Linux-x86_64_1.5.7rc1.tar.gz
You can see a new directory named ‘MGLTools-1.5.7rc1‘ has been created in the Downloads directory.
$ cd mgltools_Linux-x86_64_1.5.7rc1
$ ./install.sh
Accept the terms of the software and choose the installation folder, and click ‘Finish’ after the complete installation.
Now, in order to run this via terminal, create an alias and add it to your bashrc file using the following commands:
$ gedit ~/.bashrc
It will open the bashrc file, go to the end of this file and type the following:
$ alias adtrc='/home/user/Downloads/mgltools_x86_64Linux2_1.5.7rc1/bin/adt'
$ alias visionrc='/home/user/Downloads/mgltools_x86_64Linux2_1.5.7rc1/bin/vision'
$ alias pythonshrc='/home/user/Downloads/mgltools_x86_64Linux2_1.5.7rc1/bin/pythonsh'
Save the file, go back to the terminal, and type:
$ source ~/.bashrc
Try running adtrc
from your terminal, it should be working.
To run the Raccoon2 GUI, type the following in the terminal,
$ pythonshrc /home/user/Downloads/mgltools_x86_64Linux2_1.5.7rc1/MGLToolsPckgs/CADD/Raccoon2/gui/Raccoon2GUI.py
References
- Forli, S., Huey, R., Pique, M. E., Sanner, M. F., Goodsell, D. S., & Olson, A. J. (2016). Computational protein-ligand docking and virtual drug screening with the AutoDock suite. Nature Protocols, 11(5), 905-919.
Docking
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![[Tutorial] Installing Pyrx on Windows.](https://img.bioinformaticsreview.com/uploads/2023/04/13181032/pyrx-3.jpg)
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Docking
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Docking
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Docking
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Docking
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![[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…)
Docking
How to generate config file for docking using Autodock Tools?

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

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Docking
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Docking
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…)
Docking
How to perform metal ion-protein docking using idock?

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Docking
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Docking
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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…)
Docking
Installing PatchDock on Ubuntu (Linux)

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Docking
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Docking
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…)
Software
How to install sdsorter on Ubuntu (Linux)?

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

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Docking
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