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Installing PatchDock on Ubuntu (Linux)

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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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Dr. Muniba Faiza

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Video Tutorial: Fix broken Vina output in DS Visualizer

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Dr. Muniba Faiza

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DockingAnalyzer.py-A Python script to identify ligand binding in protein pockets.

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VS_Analysis: A Python package to perform post-virtual screening analysis

Dr. Muniba Faiza

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Bioinformatics Programming

vs_interaction_analysis.py: Python script to perform post-virtual screening analysis

Dr. Muniba Faiza

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[Tutorial] Performing docking using DockingPie plugin in PyMOL.

Dr. Muniba Faiza

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[Tutorial] Performing docking using DockingPie plugin in PyMOL.

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Docking

How to install the DockingPie plugin on PyMOL?

Dr. Muniba Faiza

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How to install DockingPie plugin on PyMOL?

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Docking

[Tutorial] Installing Pyrx on Windows.

Dr. Muniba Faiza

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[Tutorial] Installing Pyrx on Windows.

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How to install Autodock4 on Ubuntu?

Dr. Muniba Faiza

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Docking

What values are considered as good or bad in computational docking?

Dr. Muniba Faiza

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How to sort binding affinities based on a cutoff using vs_analysis.py script?

Dr. Muniba Faiza

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How to sort binding affinities based on a cutoff using vs_analysis.py script?

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Docking

Virtual Screening using Autodock Vina: Frequently Asked Questions & Answers for Starters

Dr. Muniba Faiza

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Docking

[Tutorial] How to perform docking of zinc metalloproteins using Autodock Vina?

Dr. Muniba Faiza

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[Tutorial] How to perform docking of zinc metalloproteins using Autodock Vina?

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Docking

How to generate config file for docking using Autodock Tools?

Dr. Muniba Faiza

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How to generate config file for docking using Autodock Tools?

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Docking

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

Dr. Muniba Faiza

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

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Docking

Autodock Vina: Uses & Applications

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Autodock Vina: Uses & Applications

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Docking

How to perform virtual screening using Pyrx?

Dr. Muniba Faiza

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How to perform virtual screening using Pyrx?

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Docking

How to perform metal ion-protein docking using idock?

Dr. Muniba Faiza

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How to perform metal ion-protein docking using idock?

Previously, we provided a tutorial on the installation of idock on Ubuntu (Linux). In this article, we are going to demonstrate the docking of a metal ion (such as Zn, Mg, Fe, etc.,) with a protein using idock. (more…)

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Docking

How to install idock on Ubuntu?

Dr. Muniba Faiza

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How to install idock on Ubuntu?

idock [1] is a multithreaded software based on Autodock Vina. It is a virtual screening tool for flexible ligand docking. It also supports 27 different chemical elements including zinc, magnesium, iron, calcium, etc. In this article, we are going to install idock on Ubuntu. (more…)

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Docking

How to analyze HADDOCK results using Pymol script generated from PRODIGY?

Dr. Muniba Faiza

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How to analyze HADDOCK results using Pymol script generated from PRODIGY?

In one of our previously published articles, we demonstrated protein-protein docking using HADDOCK2.4 [1]. In this article, we are going to demonstrate the HADDOCK results analysis using a Pymol script generated from the PRODIGY server [2]. (more…)

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Docking

Protein-protein docking using HADDOCK2.4 web server

Dr. Muniba Faiza

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Protein-protein docking using HADDOCK2.4 web server

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