Connect with us

Docking

Installing PatchDock on Ubuntu (Linux)

Tariq Abdullah

Published

on

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.

Docking

How to generate config file for docking using Autodock Tools?

Dr. Muniba Faiza

Published

on

How to generate config file for docking using Autodock Tools?

A configuration file is one of the required files for docking using Autodock Vina. In this article, we are going to generate a config file using Autodock Tools GUI [1]. (more…)

Continue Reading

Docking

How to install Autodock on Ubuntu (Linux) with CUDA GPU support?

Dr. Muniba Faiza

Published

on

How to install Autodock on Ubuntu (Linux) with CUDA GPU support?

Autodock [1] is most widely used for docking. To accelerate the docking process, especially, during virtual screening, Autodock-GPU [2] provides great help. In this article, we are going to install Autodock-GPU on Ubuntu. (more…)

Continue Reading

Docking

Autodock Vina: Uses & Applications

Tariq Abdullah

Published

on

Autodock Vina: Uses & Applications

Autodock Vina [1] is one of the most widely used bioinformatics software for computational docking. For beginners and those who are new to the field of bioinformatics, such software may appear confusing without having an initial idea of what this software actually used for. In this article, we have discussed some of the primary uses and applications of Autodock Vina software. (more…)

Continue Reading

LATEST ISSUE

ADVERT