OCTOBER 2019 VOL 5 ISSUE 10
“In all science, error precedes
the truth, and it is better it should go first than last.� -
Horace Walpole
Installing and executing ProtTest3 on Ubuntu
Autodock VinaXB for molecular docking of protein complexes containing halogen bonding interactions
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Contents
October 2019
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Topics Editorial....
05
03 Docking Autodock VinaXB for molecular docking of protein complexes containing halogen bonding interactions 06
05 Tips & Tricks A guide on how to read the research articles 10
04 Phylogenetics Installing and executing ProtTest3 on Ubuntu 08
FOUNDER TARIQ ABDULLAH EDITORIAL EXECUTIVE EDITOR TARIQ ABDULLAH FOUNDING EDITOR 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
Should predatory journals be eliminated completely from the research community? Muniba Faiza
EDITORIAL
Founding Editor
The fast-emergence of predatory journals is a new problem in the scientific research area. These journals send attractive advertising emails to the authors to seek money and in turn, they don't provide any proper service including a peer review for their article. As a result, they publish research studies irrelevantly for the sole purpose of draining the money down from the authors. This is affecting the research quality in the scientific field. As we all are aware of Beall's list [1] created by Jeffery Beall, an academic librarian at the University of Colorado in Denver, it lists all the predatory journals and publishers as mentioned in one of our previous articles. It represents a valuable tool for researchers to be aware of predatory journals. This list is growing continuously over time. Although Beall's list has a few shortcomings for which it has been criticized for some reasons by some researchers and publishers. These reasons include the weak methodology used by Beall's list to classify a predatory journal and some journals pointed out that Beall added newly started journals without contacting and discussing their publishing policies. Now, various scientists are objecting to the predatory journals [2] and some of them have urged publishing companies to establish their standards so that they could easily differentiate predatory journals from real scientific ones [3]. Besides, these journals are causing great harm to the scientific community. There are some predatory journals that even display a fake impact factor on their website just to attract the authors, which as compared to the real
Letters and responses: info@bioinformaticsreview.com
scientific journals is higher. This is just increasing the number of publications in scientific literature without any significant contributions. Some of the major problems and harms caused by these journals include the lack of significant information, less and irrelevant data, damaged reputation, lack of knowledge and quality control. Young researchers need to think about the harmful effects of publishing in predatory journals. What is the use of such research which can not benefit the scientific community? They must be aware of their external reputation damage as well.
EDITORIAL
Journal Citation Report (JCR) provides a list of journals with an official impact factor. But most of the new researchers are not aware of this. The question arises here is that either the predatory journals should be completely eliminated? or the scientific journals and publishers should strengthen the open-access concept and contribute significantly toward the scientific community. Further, there is a strict demand for a new system to identify predatory journals and the articles published in it. References Butler, D. (2013). Investigating journals: The dark side of publishing. Nature News, 495(7442), 433. Richtig, G., Berger, M., Lange�Asschenfeldt, B., Aberer, W., & Richtig, E. (2018). Problems and challenges of predatory journals. Journal of the European Academy of Dermatology and Venereology, 32(9), 1441-1449. Strielkowski, W. (2017). Predatory journals: Beall's List is missed. Nature, 544(7651), 416.
Write to us at info@bioinformaticreview.com.
DOCKING
Autodock VinaXB for molecular docking of protein complexes containing halogen bonding interactions Image Credit: Stock photos
“Protein data bank (PDB) [3] contains more than 200 entries of such protein complexes. This halogen bonding is used for lead optimization in rational drug design [4].� olecular docking is the most widely used technique which is used to predict the binding affinities and bound conformations of a ligand and protein complex. Autodock Vina [1] is one of the most widely used docking software for structure-based drug designing. Suppose, your multifasta file is "input.fa", in which you want to search for the motif patterns.
M
Halogen bonding interactions exist between the protein and ligands containing halogens [2]. Protein data
bank (PDB) [3] contains more than 200 entries of such protein complexes. This halogen bonding is used for lead optimization in rational drug design [4]. Most of the docking softwares do not include halogen bonding in their scoring functions and therefore, unable to successfully predict the bound conformations for such complexes. For this purpose, Autodock Vina has implemented a new halogen bonding scoring function called XBSF in a new Vina program known as Autodock
VinaXB [5]. It even provides better results than Vina [5]. Installation The installation of Autodock VinaXB is very simple. First, download the executable and then run it. The executable can be downloaded from here and the source code can be downloaded from here for Mac, Linux, and Windows as well. For Linux users, if you have trouble using the executable as it is, then, enter into the directory where you have downloaded the file, open a Bioinformatics Review | 6
terminal (Ctrl+Alt+T) and type the following commands:
halogen bond scoring function, into AutoDock Vina. Journal of cheminformatics, 8(1), 27.
$ cd Downloads $ chmod +x VinaXB Run VinaXB Autodock VinaXb has as same command-line arguments as Autodock Vina, just replace vina with VinaXB as follows: $ ./VinaXB --config conf.txt --log log.txt
Same goes with Windows, just use vinaXB.exe instead of vina.exe in the command prompt. References 1. 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. 2. 2. Auffinger, P., Hays, F. A., Westhof, E., & Ho, P. S. (2004). Halogen bonds in biological molecules. Proceedings of the National Academy of Sciences, 101(48), 16789-16794. 3. 3. Bank, P. D. (1971). Protein data bank. Nature New Biol, 233, 223. 4. 4. Sirimulla, S., Bailey, J. B., Vegesna, R., & Narayan, M. (2013). Halogen interactions in protein-ligand complexes: implications of halogen bonding for rational drug design. Journal of chemical information and modeling, 53(11), 2781-2791. 5. 5. Koebel, M. R., Schmadeke, G., Posner, R. G., & Sirimulla, S. (2016). AutoDock VinaXB: implementation of XBSF, new empirical
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PHYLOGENETICS
Installing and executing ProtTest3 on Ubuntu
Image Credit: Stock Photos
“ProtTest3 finds a best-fit model on the basis of the smallest value of one of three criterions: Akaike Information Criterion (AIC), Corrected Akaike Information Criterion, Bayesian Information Criterion (BIC) score or Decision Theory Criterion (DT) selected by the user.�
P
rottest3 is a software which is used to select a best-fit amino acid replacement model for a set of protein sequences [1]. ProtTest3 finds a best-fit model on the basis of the smallest value of one of three criteria: Akaike Information Criterion (AIC), Corrected Akaike Information Criterion, Bayesian Information Criterion (BIC) score or Decision Theory Criterion (DT) selected by the user. In this article, we will learn how to download and install the command-line version of ProtTest3 on Ubuntu.
typing the following the commands in a terminal:
odl/prottest3/downloads/pr ottest-3.2-20120316.tar.gz
$ sudo apt-get update
$ tar xvzf prottest-3.220120316.tar.gz
$ sudo apt-get upgrade
Downloading ProtTest3 A ProtTest3 package compatible with your system can be downloaded from here. We are downloading the tar file for Ubuntu. Open the terminal and change to the directory where you want to download the software, let's say 'Downloads'. $ cd Downloads
Before installing the software, update and upgrade your system by
$ wget https://bitbucket.org/dieg
If you wish to run ProtTest3 on a cluster computer, then you need to download the MPJ Express from here. Make sure you have the latest version of Java installed on your system or you can download it from here. Installing ProtTest3 After that, you will see a new directory named with 'prottest', change to that directory. $ cd prottest3
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$ set PROTTEST_HOME=/home/user/D ownloads/prottest3
<user_defined_tree_file> o <output_file> -[matrix] <models_to_evaluate> <selection_criteria> threads 4
In this directory, you will find the .jar file of ProtTest3, which you can directly use with the command line arguments on a terminal.
Executing ProtTest3 on a cluster computer If you have a large number of protein sequences in your dataset, then you can always go for cluster execution.
Installing MPJ Express After downloading the tar package, type the following commands in a terminal:
At first, start MPJ, and then run the HPC shell scripts provided in the same directory.
$ cd Downloads $ tar xvzf mpj.tar.gz $ export MPJ_HOME=$PROTTEST_HOME/mp j $ export PATH=$MPJ_HOME/bi n:$PATH
$ cd Downloads/prottest3
Executing ProtTest3
$ ./runProtTestHPC.sh <no_of_processors> <parameters>
$ mpjboot machines
For the HPC script, the basic syntax is as follows:
To run ProtTest3, you need to run the .jar file located in the prottest3 directory.
$ ./runProtTestHPC.sh 2 -i <alignment_file> -t <user_defined_tree_file> o <output_file> -[matrix] <models_to_evaluate> <selection_criteria>
$ java -jar prottest3.jar i <alignment_file> -t <user_defined_tree_file> o <output_file> -[matrix] <models_to_evaluate> <selection_criteria>
Hope this article helps!
There are many other commandline options that you can see in its manual. If you want to use multiple threads then you can do it with an additional thread option using which you can define the number of cores to be used.
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If you have any queries, then comment below or post a question here. References 1.
Darriba, D., Taboada, G. L., Doallo, R., & Posada, D. (2011). ProtTest 3: fast selection of best-fit models of protein evolution. Bioinformatics, 27(8), 1164-1165.
$ java -jar prottest3.jar i <alignment_file> -t
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TIPS & TRICKS
A guide on how to read the research articles
Image Credit: Stock Photos
â&#x20AC;&#x153;The simplest way of reading a research article as stated by Prof. Andrew Sinclair* is to start reading the abstract first. Read the abstract carefully and understand what this study is about, how it was carried out, and what are the results and conclusions that are mentioned in the last few lines of the abstract. After getting the complete idea of the study, go to the conclusion part.â&#x20AC;?
R
eading a research article could be a problem for students starting their careers in research. Research papers are sometimes difficult to understand especially when you are new to this field. In this article, we will discuss how to read and understand a research article. As we are familiar with the basic structure of a research article starting with an abstract that summarizes the whole study with a short introduction in the first two to three sentences followed by defining the attempts made in the study, results, and conclusions. After that, there is introduction
which explains the background of the study being carried out in detail and mentions all the important components, next to the introduction is methods (or methods are mentioned in the last, depending upon the guidelines provided by a journal) which explains all the experiments performed during the study and how they were carried out. After that, there are results and discussion which as it sounds, explains all the results obtained during the study and at last, conclusion defining all the derived conclusions from the whole study. The simplest way of reading a research article as stated by Prof.
Andrew Sinclair* is to start reading the abstract first. Read the abstract carefully and understand what this study is about, how it was carried out, and what are the results and conclusions that are mentioned in the last few lines of the abstract. After getting the complete idea of the study, go to the conclusion part. Read the conclusion and understand them. If you find this study interesting, then read the results section followed by the methods and materials, and then go-to discussion. Further, if you want to know more about the topic of study, then read the full introduction part.
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This way you can have a full understanding of a research article and it may also help you to read faster if you have many papers to read at the same time or looking for a particular thing. *Prof. Andrew J. Sinclair is a reputed Professor at Deakin University, Australia and an expert in Nutrition and Health. He has been recipient to many reputed awards and recently, he has been awarded the Asia Pacific Clinical Nutrition Society (APCNS) Award 2019.
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