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Docking

Installing PatchDock on Ubuntu (Linux)

Tariq Abdullah

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Installing PatchDock on Ubuntu (Linux)

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.


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 research33(suppl_2), W363-W367.

Tariq is founder of Bioinformatics Review and CEO at IQL Technologies. His areas of expertise include algorithm design, phylogenetics, MicroArray, Plant Systematics, and genome data analysis. If you have questions, reach out to him via his homepage.

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