[Tutorial] Installing jdock on Ubuntu (Linux).

jdock is an extended version of idock [1]. It has the same features as the idock along with some bug fixes. However, the binary name and the GitHub repository names are changed. We are installing jdock on Ubuntu (Linux).

Preparing system

It is good to update and upgrade your Ubuntu system first. Log into your Ubuntu system and open the terminal by pressing Ctrl+Alt+T altogether, and type the following commands:

$ sudo apt-get update

$ sudo apt-get upgrade

Installing prerequisites

To install jdock, you must have Boost installed on your system. Use the following command to install it.

$ sudo apt install libboost-program-options-dev

Downloading jdock

You can easily download jdock from the GitHub repository here or paste the following command to download via the command line.

Change to the directory where you want to download the software (in this tutorial, it’s ‘Downloads‘).

$ cd Downloads/

$ wget https://github.com/stcmz/jdock/archive/refs/heads/v2.x.zip

Installing jdock

Unzip the downloaded file.

$ unzip jdock-2.x.zip

You will notice a new directory named, jdock-2.x. Now move inside the new directory.

$ cd jdock-2.x/

Let’s install it using cmake. Ensure that you have cmake version 3.20 or higher. If not, read this article first and install the latest cmake version.

Now inside the jdock directory, run the following commands.

$ cmake -B build

$ cmake --build build --config Release

After this command, you will see

[100%] Built target jdock

Now, run this:

$ sudo cmake --install build

You should see the following on the terminal:

-- Install configuration: ""
-- Installing: /usr/local/bin/jdock

After this, run jdock as

$ jdock

It should display the usage.

References

1. Li, H., Leung, K. S., & Wong, M. H. (2012, May). idock: A multithreaded virtual screening tool for flexible ligand docking. In 2012 IEEE Symposium on Computational Intelligence in Bioinformatics and Computational Biology (CIBCB) (pp. 77-84). IEEE.