Docking
Installing GalaxyPepDock & Galaxy-Server on Ubuntu

GalaxyPepDock is a software used for protein-peptide docking based on interaction similarity. In this article, we will install GalaxyPepDock on Ubuntu.
Getting started
Let’s update and upgrade the system first.
$ sudo apt-get update
$ sudo apt-get upgrade
Remember Galaxy requires Python 3.5 or 3.6. Check your Python version python --version
. If required download or upgrade your python as shown below.
$ sudo apt-get install python3.6
$ sudo apt-get install python3.7
Downloading GalaxyPepDock
We will download GalaxyPepDock from Github.
Open a terminal (Ctrl+Alt+T) and change to the directory where you want to download the software. Let’s say Downloads and type the following command on the terminal:
$ cd Downloads/
$ wget https://github.com/seoklab/GalaxyPepDock/archive/master.zip
If you want to download it manually, then click here.
Installing GalaxyPepDock
Now, type the following commands from the same directory.
$ unzip master.zip
$ cd GalaxyPepDock-master/
$ ./install.sh
After installation completes, set environment variables.
$ sudo gedit ~/.bashrc
The file will open in an editor. Go to the end of the file and paste the following line. Remember to replace the ‘user’ with your username.
$ export GALAXY_HOME=/home/user/Downloads/GalaxyPepDock-master/
Now save it (Ctrl+S) and close. Go back to the terminal and type the following command.
$ source ~/.bashrc
Now, you have installed GalaxyPepDock on your system. You can run it by typing a complete path to the GalaxyPepDock.
Downloading Galaxy Server
$ cd Downloads/
$ wget https://github.com/galaxyproject/galaxy/archive/master.tar.gz
Installing Galaxy Server
Now, type the following commands from the same directory.
$ tar xvzf master.tar.gz
$ cd galaxy-master/
$ sh run.sh
It will take some time to finish. After that, you will be able to view Galaxy in your browser at http://localhost:8080
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…)
Docking
Basic Methodology to Predict Antigen-Antibody Interactions in silico

Antigen-antibody interactions play an important role in protecting our body from foreign molecules. This is applied in vaccine development against a disease. In this article, we are going to mention a simple methodology used in studying/ identifying interactions between antigen-antibody complex. (more…)
Docking
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…)
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