Kpax is a bioinformatics program to search and align protein structures [1]. It is currently available for Linux platforms only. In this article, we are going to install the latest version of Kpax (5.1.3) on Ubuntu (Linux).

Preparing system

Let’s update and upgrade our system first.

$ sudo apt-get update

$ sudo apt-get upgrade

Downloading Kpax

Download Kpax from here. Fill out the form and download the tar package.

Installing Kpax

Change to the directory where you have downloaded the file. Here, we have downloaded in ‘Downloads’. You will see a tar file named ‘kpax-5.1.3-x64-mint18.3.tar‘.

$ cd Downloads/

Extract the file.

$ tar xvf kpax-5.1.3-x64-mint18.3.tar

You will see a new directory named ‘kpax’. Move inside the bin directory present in kpax.

$ cd kpax/bin/

Here, you will find the executable file for kpax (kpax5.1.3.x64).

Setting variables

Now, let’s set some environment variables to run it easily from the command line.

Open bashrc file.

$ sudo nano ~/.bashrc

Go to the end of the file and add the following commands.

$ export KPAX_ROOT=/home/user/Downloads/kpax

$ export PATH=${PATH}:${KPAX_ROOT}/bin

Further, define the directories for databases and results.

$ KPAX_DATABASE=/home/user/Downloads/kpax/kpax_database

$ KPAX_RESULTS="./kpax_results/"

Now, save and exit the bashrc file.

$ source ~/.bashrc

Kpax will write its output to a sub-directory named kpax_results.

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References

1. Ritchie, D. W., Ghoorah, A. W., Mavridis, L., & Venkatraman, V. (2012). Fast protein structure alignment using Gaussian overlap scoring of backbone peptide fragment similarity. Bioinformatics, 28(24), 3274-3281.