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Docking

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

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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

  1. 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.

Tariq is founder of Bioinformatics Review and CEO at IQL Technologies. His areas of expertise include algorithm design, phylogenetics, MicroArray, Plant Systematics, and genome data analysis. If you have questions, reach out to him via his homepage.

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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

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Docking

[Tutorial] Installing Pyrx on Windows.

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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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How to perform virtual screening using Pyrx?

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Docking

How to perform metal ion-protein docking using idock?

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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?

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Docking

Installing PatchDock on Ubuntu (Linux)

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Installing PatchDock on Ubuntu (Linux)

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Docking

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Dr. Muniba Faiza

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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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Software

How to install sdsorter on Ubuntu (Linux)?

Dr. Muniba Faiza

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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?

Dr. Muniba Faiza

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

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