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).

Preparing system

Open a terminal by pressing Ctrl+Alt+T. Update and upgrade your system using the following commands:

$ sudo apt-get update

$ sudo apt-get upgrade

Downloading PatchDock

To download PatchDock, you will have to fill out a small form providing your name, email address, and affiliation. Then you will get a link to download the zip file of the latest version of the software. You can fill out the form here.

Download the software in a directory. For this tutorial, we are downloading in let’s say, ‘Downloads‘.

Installing PatcDock

Change to the directory where you have downloaded the zip file.

$ cd Downloads/

Now unzip the downloaded file using the following command.

$ unzip patch_dock_download.zip

It will create a new directory namely, PatchDock, move inside this new directory.

$ cd PatchDock/

Now, you just have to copy the Linux executable file to your /usr/bin/ directory as shown below.

$ cp patch_dock.linux /usr/bin/

Now the PatchDock is successfully installed on your system.

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References

1. Duhovny, D., Nussinov, R., & Wolfson, H. J. (2002, September). Efficient unbound docking of rigid molecules. In International workshop on algorithms in bioinformatics (pp. 185-200). Springer, Berlin, Heidelberg.
2. Schneidman-Duhovny, D., Inbar, Y., Nussinov, R., & Wolfson, H. J. (2005). PatchDock and SymmDock: servers for rigid and symmetric docking. Nucleic acids research, 33(suppl_2), W363-W367.