BIOINFORMATICS REVIEW-FEBRUARY 2020

FEBUARY 2020 VOL 6 ISSUE 2

“Men love to wonder, and that

is the seed of science ” -

Ralph Waldo Emerson

How to install DeepView-Swiss PDB Viewer on Linux?

How to install DeepView-Swiss PDB Viewer on Linux?

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Contents

February 2020

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Topics Editorial....

03 Structural Bioinformatics How to install DeepView-Swiss PDB Viewer on Linux?

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FOUNDER TARIQ ABDULLAH EDITORIAL EXECUTIVE EDITOR TARIQ ABDULLAH FOUNDING EDITOR Dr. MUNIBA FAIZA SECTION EDITORS FOZAIL AHMAD ALTAF ABDUL KALAM MANISH KUMAR MISHRA SANJAY KUMAR PRAKASH JHA 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: New perspectives for BiR with a new year

EDITORIAL EDITORIAL

Welcoming BiR into a new year full of goals, new developments, and achievements. This year’s resolution of BiR is to take this endeavor to a brand new platform of international standard and reputation necessary for spreading the knowledge of bioinformatics.

Dr. Muniba Faiza

Founding Editor

As bioinformatics is growing and gaining more and more interest in biological research, it has become an essential field in the last few years. Researchers are capable of tracking evolutionary history, designing new drugs, study the nature of organisms, and so on. Keeping that in mind, this year BiR is going to focus on advanced research in bioinformatics. BiR is hoping to organize internship programs and conferences to reach out to experts in bioinformatics.

Besides, new tutorials will be provided both written and video tutorials as per the suggestions of our readers and subscribers. In this aspect, BiR thus seeks viewpoints and suggestions from all the readers. We would greatly appreciate that! We wish for a number of contributions from our readers in the form of articles or questions, and feedback to further improve the science reporting.

With the support of our readers, we can easily move further. BiR is thankful to all of you and wishes you a very happy new year with great success ahead.

Please share your thoughts at info@bioinformaticsreview.com.

Letters and responses: info@bioinformaticsreview.com

STRUCTURAL BIOINFORMATICS

How to install DeepView-Swiss PDB Viewer on Linux?

Image Credit: Stock photos

“In this article, we will install DeepView on Linux (Ubuntu).� eepView (Swiss-PDB Viewer) [1] is used to analyze multiple proteins simultaneously.

Protein structure alignment, active site comparison, amino acid mutations, Hbonds, and other relevant functions can be easily performed using this software [1].

D

dbv/program/spdbv37sp5Linux.tar.gz

Installing Open a terminal and change to the directory where you have downloaded the software. Let's say here it is 'Downloads'. $ cd Downloads

Preparing At first, update and upgrade your system using the following commands: $ sudo apt-get update $ sudo apt-get upgrade

Downloading Download the software from here or use the command line as shown below: $ sudo wget http://www.genebee.msu.su/sp

$ tar xvf spdbv37sp5Linux.tar $ ./install.sh

in your system, it is assumed here that these libraries are present in /usr/lib/.) $ ln -s /usr/lib/libGL.so.1.2.0 /usr/lib/libMesaGL.so.3 $ ln -s /usr/lib/libGLU.so.1.2.0 /usr/lib/libMesaGLU.so.3

References 1.

Kaplan, W., & Littlejohn, T. G. (2001). SwissPDB viewer (deep view). Briefings in bioinformatics, 2(2), 195-197.

Sometimes, an error may occur regarding the loading of shared libraries, libMesaGL.so.3. These libraries are linked with DeepView which are now called libGL.so.3 and libGLU.so instead of libMesaGL.so and libMesaGLU.so.

If you encounter this error, then make some symbolic links to the old names as shown below: (Locate the libraries Bioinformatics Review | 6

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