BIOINFORMATICS REVIEW- JULY 2018

JULY 2018 VOL 4 ISSUE 7

“Scientists have become the bearers of the torch of discovery in our quest for knowledge.”

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Stephen Hawking

Do we need more bioinformaticists or Bioinformaticians?

Prediction of biochemical reactions catalyzed by enzymes in humans

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Contents

July 2018

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Topics Editorial....

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03 Algorithms Prediction of biochemical reactions catalyzed by enzymes in humans

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04 Featured Do we need more bioinformaticists or Bioinformaticians?

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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

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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

Bioinformatics- A broad future ahead: Editorial

EDITORIAL

It has been a wonderful time since BiR came into existence. As we enter a new year, BiR tries to look forward towards the development and wonderful achievements and providing the best knowledge regarding bioinformatics. In the past two years, BiR has hit a long road from a few readers to several thousand.

Muniba Faiza

Founding Editor

Every complimentary and appreciation mail we get feels like an achievement for us. Bioinformatics has got a great future ahead of it with a better understanding and precise methodologies for both dry and the wet lab experimentations.

In the last two years, BiR has advanced in many aspects. We have come up with an android app which helps our readers to stay connected with the latest updates, our articles have started to appear in Google Scholar, we get a lot of cherishing emails, and collaboration proposals. BiR is trying to broaden the horizons by covering different domains of bioinformatics. Since bioinformatics is multidisciplinary, to date, the team of BiR has tried to go through almost every aspect of it including big data, sequence analysis, structural bioinformatics, data mining, tools, software, biostatistics, and so on. This year BiR is more focused to provide a rich content to our readers and help to understand the concepts of bioinformatics more easily. The team of BiR is trying to reach to the students to encourage them for their career in bioinformatics and to the researchers currently working in the same area. The last internship at BiR was a great success and we got an amazing response from our interns. We are looking forward to presenting our work at school and college level to introduce this to the young minds who are more fascinated by the technology.

We have such a long road to drive on which is not possible without the support of our readers, subscribers, and contributors. We are thankful to our readers wholeheartedly for their support and suggestions and wish them a very happy and prosperous new year

Letters and responses: info@bioinformaticsreview.com

with new hopes and great achievements. We would like to hear your thoughts and feedback about BiR, and what other kinds of articles you would like to read.

EDITORIAL

Please write us at info@bioinformaticsrevew.com

ALGORITHMS

Genome editing of human embryos using CRISPR/Cas9crossing the ethics of gene editing?

Image Credit: Stock Photos

“The basic requirement for using any bioinformatics software/tool is the file format and it is very difficult to deal with the phylogenetic tree conversions for the beginners sometimes. There are a bunch of tools available to visualize and annotate phylogenetic trees.” here are many biological important enzymes which exist in the human body, one of them is Cytochrome P450 (CyP450) enzymes which are mostly considered in drug discovery due to their involvement in the majority (75%) of drug metabolism [1].

Therefore, various insilico methods have been applied to predict the possible substrates of CyP 450 enzymes [2-4]. Recently, an insilico model has been developed to predict the potential chemical reactions mediated by the enzymes present in humans including CyP450 enzymes [5].

T

This method is based on descriptors calculation and supervised machine learning. The pipeline utilizes two databases: Human Metabolome

Database (HMDB) and Braunschweig Enzyme Database (BRENDA) as training datasets, and DrugBank as the test dataset.

The physicochemical properties of a query molecule are matched with the substrates obtained from the databases and then assumed to be catalyzed by as the same enzyme as the matched substrate. PaDELDescriptor is used to calculate the chemical and physical properties of substrates [6]. Similarly, all the matched substrates are found from the databases and the query molecule is scored according to the integrated scoring method, which captures the distribution of individual scores by assigning a positive weight to the scores higher than the average [5].

Four different machine learning algorithms are applied in this pipeline:

artificial neural network, naïve Bayes, multiple linear regression, and random forest which are used for cross-validation to obtain the best model. Further, the performance is validated by the test dataset, i.e., DrugBank.

According to their performance evaluation, this prediction model can successfully predict the enzymatic reactions for substrates (query molecules) and can also be applied to find some other biologically relevant reactions catalyzed by human enzymes [5].

References 1.

Guengerich, F. P. (2007). Cytochrome p450 and chemical toxicology. Chemical research in toxicology, 21(1), 70-83.

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2.

Yap, C. W., Xue, Y., & Chen, Y. Z. (2006).

Application of support vector machines to in silico prediction of cytochrome p450 enzyme substrates and inhibitors. Current topics in medicinal chemistry, 6(15), 1593-1607.

3.

Jensen, B. F., Vind, C., Padkjær, S. B., Brockhoff, P. B., & Refsgaard, H. H. (2007). In silico prediction of cytochrome P450 2D6 and 3A4 inhibition using Gaussian kernel weighted knearest neighbor and extended connectivity fingerprints, including structural fragment analysis of inhibitors versus noninhibitors. Journal of medicinal chemistry, 50(3), 501-511.

4.

Olsen, L., Oostenbrink, C., & Jørgensen, F. S. (2015). Prediction of cytochrome P450 mediated metabolism. Advanced drug delivery reviews, 86, 61-71.

5.

Yu, M. S., Lee, H. M., Park, A., Park, C., Ceong, H., Rhee, K. H., & Na, D. (2018). In silico prediction of potential chemical reactions mediated by human enzymes. BMC bioinformatics, 19(8), 207.

6.

Yap, C. W. (2011). PaDEL‐descriptor: An open source software to calculate molecular descriptors and fingerprints. Journal of computational chemistry, 32(7), 1466-1474.

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FEATURED

Do we need more bioinformaticists or bioinformaticians?

Image Credit: Google Images

“It is very important to analyze information from data efficiently, Bioinformaticians, with no doubt, have a keen sense of bioinformatics tools and software's applications under variable conditions to obtain better results. In this era, where genomic data is increasing enormously, we surely need more management techniques, interfaces, and efficient software to deal with it.� s we all know the major difference between a bioinformaticist and a bioinformatician is that a bioinformaticist is an expert in developing software, tools, interfaces for effective use of these tools with a pure knowledge of their usage, on the other hand, a bioinformatician is a skilled person with knowledge of the application of these tools and software without a deeper understanding of their workflows.

A

It is very important to analyze information from data efficiently, Bioinformaticians, with no doubt, have a keen sense of bioinformatics tools and software's applications under variable conditions to obtain better results. In this era, where genomic data is increasing enormously, we surely need more management techniques, interfaces, and efficient software to deal with it.

For example, when it comes to analyzing data, a file full of half a trillion bases cannot be opened in Excel as it is limited to open only up to one million lines. At this stage in the world, research should not be suffered through technology limits.

Besides, those who are transitioning from wet to dry lab in academic and pharmaceutical research settings can be trained and can be provided with sharp usage and knowledge of bioinformatics tools. A programme was launched at USC's Department of Transitional Genomics (https://dtg.usc.edu/site/index.php/b ioinformatics/) to train those transitioning candidates. But still in order to get more and better pieces of equipment, one needs to develop them and here come the bioinformaticists.

Indeed it takes a lot of hard work to develop such platforms, software, and interfaces to facilitate the work of bioinformaticians and experimentalists but they are always advancing in techniques which provide better tools to study, understand and resolve the problem. Besides, there is also a great demand for bioinformaticians as well because complex data analysis plays an important role in discoveries. Thus, both bioinformaticists and bioinformaticians come under the most valued persons in academics, health care, and industries such as pharmaceuticals.

There is an increasing demand for both bioinformaticists as well as for bioinformaticians, however, it takes a lot of computational skills to be a bioinformaticist. Also, in order to get more bioinformaticians and bioinformaticists, there must be more Bioinformatics Review | 9

training programs which can help candidates to better understand the mechanisms and develop better platforms to ultimately get answers for problems in the biological world.

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