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
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…)
You must be logged in to post a comment Login