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.
Getting started
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
Downloading Autodock4.2.6
You can download it either directly by visiting the website or using the command line as follows. I am downloading it in the ‘Downloads‘ folder, so first, move inside this directory.
$ cd Downloads/
$ wget https://autodock.scripps.edu/wp-content/uploads/sites/56/2021/10/autodocksuite-4.2.6-x86_64Linux2.tar
Installation
Type the following command in the terminal:
$ tar xvf autodocksuite-4.2.6-x86_64Linux2.tar
This will create a new directory called “x86_64Linux2” in the Downloads directory, in which we can see two executable files: “autodock4” and “autogrid”.
We will move them to another directory where we keep the binaries.
$ cd x86_64Linux2/
$ sudo mv autodock4 /usr/local/bin
$ sudo mv autogrid4 /usr/local/bin
Now, you have successfully installed the Autodock suite on Ubuntu.
References
- Morris, G. M., Huey, R., Lindstrom, W., Sanner, M. F., Belew, R. K., Goodsell, D. S., & Olson, A. J. (2009). AutoDock4 and AutoDockTools4: Automated docking with selective receptor flexibility. Journal of computational chemistry, 30(16), 2785-2791.
- Santos-Martins, D., Solis-Vasquez, L., Tillack, A. F., Sanner, M. F., Koch, A., & Forli, S. (2021). Accelerating AutoDock4 with GPUs and gradient-based local search. Journal of Chemical Theory and Computation, 17(2), 1060-1073.
