Docking
Installing MGLTools2 package (ADFR/AGFR/AutoSite) on Ubuntu

MGLTools2 package comes with three different tools for docking: ADFR, AGFR, and AutoSite [1-3]. In this article, we will install this package on Ubuntu.
Getting started
Let’s update and upgrade the system first.
$ sudo apt-get update
$ sudo apt-get upgrade
Downloading MGLTools2
Change to the directory where you want to download and install the software. Let’s say, Downloads. Open a terminal (Ctrl+Alt+T) and type the following commands. Don’t forget to check the architecture of your system first whether it is 32-bit or 64-bit and then download accordingly. Click here to select an appropriate package.
$ cd Downloads/
$ wget http://adfr.scripps.edu/AutoDockFR/installers/mgltools2_x86_64Linux2_1.0.tar.gz
Installing MGLTools2
We are in the same directory (i.e., Downloads). Now extract the downloaded package and install using the following commands.
$ tar xvzf mgltools2_x86_64Linux2_1.0.tar.gz
$ cd mgltools2_x86_64Linux2_1.0/
$ ./install.sh
Adding in the path
Now add this in your path as shown below.
$ export PATH=/home/muniba/Downloads/billi/mgltools2_x86_64Linux2_1.0/bin:$PATH
Creating aliases
Open the bashrc file and add the following at the end of the file.
$ sudo gedit ~/.bashrc
It will open your bashrc file in gedit. Scroll to the end of the file and add the following commands:
$ alias adfr='sudo /home/user/Downloads/mgltools2_x86_64Linux2_1.0/bin/adfr'
$ alias agfr=' sudo /home/user/Downloads/mgltools2_x86_64Linux2_1.0/bin/agfr'
$ alias autosite=’sudo /home/user/Downloads/mgltools2_x86_64Linux2_1.0/bin/autosite’
Don’t forget to replace the user
in the above commands with your username.
$ source ~/.bashrc
Now you can execute these three tools by typing their aliases in the terminal. For example,
$ adfr
$ agfr
$ autosite
References
- Ravindranath, P. A., Forli, S., Goodsell, D. S., Olson, A. J., & Sanner, M. F. (2015). AutoDockFR: advances in protein-ligand docking with explicitly specified binding site flexibility. PLoS computational biology, 11(12), e1004586.
- Zhao, Y., Stoffler, D., & Sanner, M. (2006). Hierarchical and multi-resolution representation of protein flexibility. Bioinformatics, 22(22), 2768-2774.
- Ravindranath, P. A., & Sanner, M. F. (2016). AutoSite: an automated approach for pseudo-ligands prediction—from ligand-binding sites identification to predicting key ligand atoms. Bioinformatics, 32(20), 3142-3149.
Docking
[Tutorial] Performing docking using DockingPie plugin in PyMOL.
![[Tutorial] Performing docking using DockingPie plugin in PyMOL.](https://img.bioinformaticsreview.com/uploads/2023/10/25151930/dockingpie1.jpg)
DockingPie [1] is a PyMOL plugin to perform computational docking within PyMOL [2]. In this article, we will perform simple docking using DockingPie1.2.
Docking
How to install the DockingPie plugin on PyMOL?

DockingPie [1] is a plugin of PyMOL [2] made to fulfill the purpose of docking within the PyMOL interface. This plugin will allow you to dock using four different algorithms, namely, Vina, RxDock, SMINA, and ADFR. It will also allow you to perform flexible docking. Though the installation procedure is the same for all OSs, in this article, we are installing this plugin on Ubuntu (Linux).
Docking
[Tutorial] Installing Pyrx on Windows.
![[Tutorial] Installing Pyrx on Windows.](https://img.bioinformaticsreview.com/uploads/2023/04/13181032/pyrx-3.jpg)
Pyrx [1] is another virtual screening software that also offers to perform docking using Autodock Vina. In this article, we will install Pyrx on Windows. (more…)
Docking
How to install Autodock4 on Ubuntu?

Autodock suite is used for docking small molecules [1]. Recently, Autodock-GPU [2] 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.
Docking
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…)
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…)
Docking
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…)
Docking
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…)
Docking
Autodock Vina: Uses & Applications

Autodock Vina [1] 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…)
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?

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. (more…)
Docking
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…)
Docking
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…)
Docking
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…)
Docking
Protein-protein docking using HADDOCK2.4 web server

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…)
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)?

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…)
Docking
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…)
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