BIOINFORMATICS REVIEW- AUGUST 2017

AUGUST 2017 VOL 3 ISSUE8

“The most beautiful thing we can experience is the mysterious. It is the source of all true art and science.”

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Albert Einstein

How to install AutoDock Vina on Ubuntu?

AutoDock Vina tutorial

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Contents

August 2017

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Topics Editorial....

03 Tutorial How to install AutoDock Vina on Ubuntu?

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FOUNDER TARIQ ABDULLAH EDITORIAL EXECUTIVE EDITOR TARIQ ABDULLAH FOUNDING EDITOR MUNIBA FAIZA SECTION EDITORS FOZAIL AHMAD ALTAF ABDUL KALAM MANISH KUMAR MISHRA SANJAY KUMAR NABAJIT DAS REPRINTS AND PERMISSIONS You must have permission before reproducing any material from Bioinformatics Review. Send E-mail requests to info@bioinformaticsreview.com. Please include contact detail in your message.

BACK ISSUE Bioinformatics Review back issues can be downloaded in digital format from bioinformaticsreview.com at $5 per issue. Back issue in print format cost $2 for India delivery and $11 for international delivery, subject to availability. Pre-payment is required CONTACT PHONE +91. 991 1942-428 / 852 7572-667 MAIL Editorial: 101 FF Main Road Zakir Nagar, Okhla New Delhi IN 110025 STAFF ADDRESS To contact any of the Bioinformatics Review staff member, simply format the address as firstname@bioinformaticsreview.com PUBLICATION INFORMATION Volume 1, Number 1, Bioinformatics Reviewâ„¢ is published monthly for one year (12 issues) by Social and Educational Welfare Association (SEWA)trust (Registered under Trust Act 1882). Copyright 2015 Sewa Trust. All rights reserved. Bioinformatics Review is a trademark of Idea Quotient Labs and used under license by SEWA trust. Published in India

EDITORIAL

Bioinformatics Review (BiR): Bridging Between The Two Worlds Informatics and Biology are two sciences which are as different from each other as possible. One runs on the core concept of variation and another on strict reasoning. But still, these two have combined in a most natural way under the realm of “Bioinformatics”. For a biologist today it’s difficult to imagine a world without all biological databases and further no branch to decipher the huge enigma that it brings. Bioinformatics Review (BiR) journal is a platform to discover the latest happenings in this melting pot of two varied fields.

Dr. Roopam Sharma

Honorary Editor

The era of “omics” kick-started with the drafting of Human Genome Project (HGP) in 2003. Since then, a number of technological advancements especially, NGS has been generating mind-boggling data for the knowledge banks. Latest inventions like single-cell transcriptomics or metagenomics of most unusual habitats show how the evolution of technological advancements is directly resulting in breakthroughs in biological sciences.

Among various areas of biology which has benefited from these advancements is Pathology. In fact, deciphering the molecular and genetic basis of diseases in humans was the guiding force behind human genome sequencing Project. Bioinformatics has led to an impressive increase in recognition of possible pathogenic factors in varied systems, so much so that new techniques are being devised to increase the speed to actually test these factors in the wet lab. If we consider computationally, smaller but ever-changing genomes and transcriptomes of these pathogens, make them a much suitable candidate to test out many hypotheses for Bioinformatics studies. Effector Bioinformatics involves building custom pipelines for distinct species based on characteristics of effectors and size of the genome involved. These can be based on

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EDITORIAL

Homology or feature extraction or both, e.g. discovery of RXLR motifs in Oomycete effectors allowed many more effectors to be identified. This collaboration of two sciences for plant pathology has led to the development of many general use platforms like Broad-Fungal Genome Initiative, EuPathDB, PhytoPath and so on, but there is much need of developing specified resources like PHIbase for specific areas like effector biology. The use of machinelearning techniques like artificial neural network approach (which is actually based on biological neural networks) really shows how the two branches are so distinct yet so intertwined. All in all, it’s a brave new world where artificial communication is not only stimulating but also helping us understand the communication (between host and pathogen) going within the realm of life.

In this issue, BiR focusses on reviews related to some of the very basic techniques which have been used in computational biology and its applications in various biological studies. We look forward to continued support from our readers and contributors. For suggestions and feedback, do write to us at info@bioinformaticsreview.com

TUTORIAL

How to install AutoDock Vina on Ubuntu?

Image Credit: Stock Photos

“In this small tutorial, we will learn how to install AutoDock Vina on Ubuntu.�

utoDock Vina is one of the most popular software in Bioinformatics, known for the molecular docking simulations. I have already explained the docking procedure in my previous article. In this small tutorial, we will learn how to install AutoDock Vina on Ubuntu. Its installation on Ubuntu may be a tedious process, especially for the beginners due to the unfamiliarity of the Linux commands. It is expected to work on any version of Ubuntu but make sure whether your system supports the 32- bit or 64- bit version. If you face any problem, then feel free to ask.

1. MGL Tools (AutoDock Tools are important as they provide the GUI)

You need a good Internet connection as you will have to download different files. We need to download the following software to install AutoDock Vina:

$ sudo apt-get update $ sudo apt-get upgrade

A

2. AutoDock Vina 3. Python 4. AutoDock4 5. Autogrid 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:

Downloading the files

Now we are going to download the above-mentioned files one by one.

You can download them either directly by visiting the websites or you can download using the command line as follows. It basically downloads in the 'Downloads' folder, so we will enter into this directory and download the files using the command line. $ cd Downloads/ $ wget http://mgltools.scripps.edu /downloads/tars/releases/RE L1.5.6/mgltools_i86Linux2_1 .5.6.tar.gz $ wget http://vina.scripps.edu/dow nload/autodock_vina_1_1_2_l inux_x86.tgz

It is good to install python PIL because most of the times it prompts

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an error for imaging C module during the installation. $ wget http://effbot.org/downloads /Imaging-1.1.7.tar.gz

In my case, this issue was not resolved even after installing the imaging C module, then I installed the following library and it resolved my case. If you also get the same error even after installing python imaging library, then try the following: $ sudo apt-get libjpeg62:i386

install

Although AutoDock Vina can run without installing AutoDock4 and Autogrid, you will need them if you run the AutoDock4 analysis from AutoDock Vina itself. Therefore, it is better to install them. In order to download them, you will have to type the following commands: $ sudo wget http://autodock.scripps.edu /downloads/autodockregistration/tars/dist426/a utodocksuite-4.2.6i86Linux2.tar

To install them, open the terminal and go to the Downloads folder again. $ cd Downloads $ tar xvf autodocksuite4.2.6-i86Linux2.tar

This will create a new directory called "i86Linux2" in the Downloads directory, in which we could see two executable files: "autodock4" and "autogrid". We will move them to another directory where we keep the binaries. $ cd $ sudo mv /usr/local/bin $ sudo mv /usr/local/bin

i86Linux2 autodock4 autogrid4

Now we will come back to our Downloads directory to install the rest of the files. Let's install mgltools. $ cd Downloads $ tar xvzf mgltools_i86Linux2_1.5.6.ta r.gz

This will extract files of mgl tools and create a folder named "mgltools_i86Linux2_1.5.6". Now to install it, we will go to the mgl tools directory.

Installation

$ cd mgltools_i86Linux2_1.5.6 $ ./install.sh

Now that we have the tar files in the Downloads folder, we will extract and install them one by one. Let's install AutoDock suite first, then later the MGL tools, and AutoDock Vina.

During installation, a dialog box will prompt on your screen, its the license agreement, so just click "Ok".

If everything goes well, then the terminal will show "MGLTools installation complete". It will also ask

to create aliases to run them because it's a tedious task to write the full path every time we run them. So it is convenient to create aliases which I will tell you a little later after we finish installation of AutoDock Vina.

We have installed mgl tools on the system, now we will go for AutoDock Vina. To do that, let's go back to our Downloads folder, where we downloaded the tar files. $ cd Downloads/ $ tar xvzf autodock_vina_1_1_2_linux_x 86.tgz

After extracting the tar file of AutoDock Vina, you will see a folder in your Downloads directory named "autodock_vina_1_1_2_linux_x86", which consists of a bin folder where you could see two setup files for vina: "vina" & "vina_split".

This ends the installation section of our tutorial. Now we have successfully installed AutoDock Vina on Ubuntu. In the following section, I will tell you how to create aliases for the paths.

Creating aliases If you would see the README file in the bin folder of mgl tools, it shows the paths for running the autodock tools and python molecular viewer.

Using these paths, we will create aliases and to use them permanently we will add them in the bashrc file.

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Open the terminal and type the following commands: $ gedit ~/.bashrc

It will open the bashrc file, go at the end of this file and type the following: alias adt='sudo /home/username/Downloads/mg ltools_i86Linux2_1.5.6/bin/ adt' alias pmv='sudo /home/username/Downloads/mg ltools_i86Linux2_1.5.6/bin/ pmv'

Save the file, go back to the terminal and enter the following command: $ source ~/.bashrc

Now, whenever you will type 'adt' or 'pmv', it will open the autodock vina or pymol viewer respectively.

We are all done! You can perform docking on your Ubuntu system using AutoDock Vina whenever you want. :)

References Trott, O., & Olson, A. J. (2010).

AutoDock Vina: improving the speed and accuracy of docking with a new scoring function, efficient optimization, and multithreading.

Journal of computational chemistry, 31(2), 455-461.

For any query, you can comment below, or email me at muniba@bioinformaticsreview.com.

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