Author: Amal A.M.
A researcher, Ph.D. graduate (Biotechnology), Editor, Tutor, Teacher and a Baker.

Molecular Docking : A Starter Pack

Molecular Docking : A Starter Pack

Let's learn docking together

Molecular Docking : A Starter Pack


1.How to install AutoDock Vina on Ubuntu
2.How to install PyMol on Ubuntu
3.How to perform protein-ligand docking using AutoDock Vina
4.How to analyze AutoDock Vina results using PyMol.

About the Speaker

Dr. Oualid Bellag

Biotechnology Engineering, Molecular Biology

Oualid Bellag is a biologist and geneticist by formation. His research interest is directed toward directed evolution of enzymes and synthetic biology with application in chemical, pharmaceutical and agriculture industries. He is involved in teaching and training of different subjects, such as molecular biology, enzymology, bioinformatics and many more.

Emailing your Academic Supervisor; DO and DON’T: PART I

Have you ever had a moment when you emailed your supervisor, especially your academic supervisor, but soon after, regret starts to hit and you start thinking “should I have used this word here?” or “God! Is this even appropriate?”

Did you receive a very short and rude reply? Do you think you should write more or less? Or maybe you are conflicted on what type of language you should be using. Should you write in a formal or semi-formal style?



We are with you! Let us go through this hassle together with real-life examples that I have acquired after many trials and errors during my research journey.

I presume you have settled your mind and chosen the potential advisor you want to work with. However, have you thought about how to approach him or her? I believe that is the first challenge and it could be the first step toward your future work with those academicians.

Usually, professors are busy as they have piles of tasks to accomplish in a very short time. Frankly speaking, over time, you will be the one handling all the work one way or the other (you have been warned!). Professors need to deal with publications (books, articles, conferences) as well as giving lectures. On top of that, they also need to secure a research fund to continue their research. The path is not as easy as you may think.

So, your first step is to give an introduction about yourself. You want to be clear, concise and polite. I would prefer a formal email at the beginning as it will show respect. However, it depends on the country and the culture as some do not really grasp formal emails, and they find it heavy to digest. I suggest you familiarize yourself with the culture of the intended location which would give you the advantage of being somewhat acquainted with the recipient of your email.

How to start?

If you know the name of the advisor, it is good to directly email him/her. However, sometimes, you might need to email the head of the department or the head of the research unit as the information might not be disclosed.

The more information you can obtain, the better it will be. At the minimum, you should know the title, name, and background of the publications and research interests.

Start with:

Dear Professor/ Dr [NAME],

Do not assume that the professors or the assistant professors are all married, so avoid starting with Mrs. and Ms as it might be improper and inconvenient.

Again, do not greet them the usual way, such as: good morning, good afternoon, good evening. There is a chance they are not reading your email in the morning or in that specified time, therefore, skip that phrase.

What is next?

You did your research, and you are now selling yourself and your skills.

Introduce yourself briefly inferring where you graduated from and your major.  After that, make a clear statement of your purpose of writing.

For example,

Dear Professor Smith,

I am writing in regard to the announced Ph.D. positions in [Microbiology], announced on your web page. I graduated from [Sunway University], with an MSc degree in Biochemistry.  My research’s focus was on the production of microbial lipases from agricultural wastes.

That should be enough for the introduction.

What is next?

Show the professor that you have done some research on the background of his/her interest. You could read a few of his/her recent publications (3 or 4 will do) and mention that in your email. This would give an indication that you have a similar research interest and you have made an effort to look into it.

For example,

I have read your articles [mention them as references at the end] on purification of lipases using new technology. I have published two review articles on enzyme purification methods, and I would like to continue exploring this area. Your recent article [XXX] regarding the green approach of purification grabbed my attention, and I have a few ideas to expand this work in many aspects.

Now comes the core

Explain exactly what you want to do.

For example,

Thus, I am quite interested to join the research center at your institute. I would like to know if there is any chance for me to pursue my Ph.D. under your supervision.


As you are coming to an end, you need to mention what you have attached with your email and any other remarks. Thank the professor for the time taken to read and consider your application and sign out.

For example:

As you are approaching the end, you need to mention what you have attached with your email and any other remarks. Thank the professor for the time taken to read and consider your application and sign out.

I look forward to your response.

Sincerely yours,

[Eyma GH]

I hope your inbox will have a positive reply with the next post date.

Good Luck!



Dr. Amal A. M. &  Ms. Asmaa A.

The Strategies to Publish in High-impact Journals

Editors at top journals are looking for specific components that may not be the author’s focus point.

First, the editor will take a look at your title, then your abstract. If those two components are satisfying, the editor will send the article for the review process. The content of the paper is usually not checked by the editor and does not give the first impression.


Make your title appealing. It is recommended to give a long title, enough to understand the aim of your article. It should not be very long, or otherwise, the reader might lose interest before reaching your content.



Focus on making your abstract informative. The findings of your research should be highlighted rather than introducing the background of the study. Many of the reviewers gave me useful tips. Some recommend providing one statement describing the research idea. This is followed by a summary of the methodology. Then, state your findings, particularly the breakthrough of the research. End your abstract with a final statement to conclude the contribution of this paper.

Graphical Abstract

Though not mandatory, a graphical abstract is a tool to summarize the idea in a diagram or a figure. Some journals obligate the authors to submit graphical abstracts with instructions. See the two example below (Fig. 1).

Fig. 1. A graphical abstract expresses the differences between one-step and two-step saccharification of biomass (Elgharbawy et al., 2016). © 2016 Elsevier B.V. All rights reserved.

You can observe that the drawing is not fancy nor sophisticated. We simply used Adobe Photoshop basic tools and MS Powerpoint to generate the abstract.


Fig. 2. A graphical abstract to summarize the ionic liquids applications integrated with lipases (Elgharbawy et al., 2018). © 2017 Elsevier B.V. All rights reserved.

We used MS Powerpoint to generate the Fig. 2.


You are writing your article to be read. Make it clear and straightforward. Audience from several backgrounds should be able to understand 25% of your article. Do not present your ideas in complicated vocabularies while the content is misleading (Gould, 2014).

During my Ph.D. journey, I have received several comments from the reviewers. They recommend focussing your energy on drawing your introduction carefully. This aims to show your “state-of-the-art” in this research.  It simply means to give the best available. Provide the reader with a concise background, followed by the research gaps and what you offer in this context. This will assist you to find the direction to list your findings.

Do not use figures and tables to illustrate the same findings. You should be able to distinguish which should be better shown in figures/tables and which could be described in the text.

Remember that you have limited number of figures and tables. Some journals restrict you to 5-6 figures, so choose wisely.


This is a summary of your work. Provide the outcome of your research and the future outlook that might lead to possible investigations. Do not repeat the abstract.



Most of the writers miss one or two “in-text citation.” Carefully cross-check your references list with the text. Make sure to follow the reference style from your targeted journal.


Stay tuned. We have more for you.

Happy writing


  • Elgharbawy, A. A., Riyadi, F. A., Alam, M. Z., & Moniruzzaman, M. (2018). Ionic liquids as a potential solvent for lipase-catalysed reactions: A review. Journal of Molecular Liquids, 251.
  • Elgharbawy, A. A., Alam, M. Z., Moniruzzaman, M., & Goto, M. (2016). Ionic liquid pretreatment as emerging approaches for enhanced enzymatic hydrolysis of lignocellulosic biomass. Biochemical Engineering Journal, 109, 252–267.
  • Gould, Julie. “How to Get Published in High-Impact Journals: Big Research and Better Writing.” Nature News, Nature Publishing Group, 3 Nov. 2014,

How to improve your writing skills

Learn or Practice?

Learning a variety of writing skills isn’t as difficult as you may think.
Becoming a better writer takes practice, and you’re already practicing. No, seriously—you write a lot. Even if you don’t think of yourself as a writer, you put thoughts into text more often than you realize. At the very least, you write emails, post on social media, make updates to your resume and profiles and message your friends. If your job requires it, you also create things like reports, presentations, newsletters . . . it’s a long list.

So, you’re already writing. Now, improving your writing skills is just a matter of becoming conscious of the things you can do to give your text more structure and make your copy crisp and readable with a conversational style [1].

Continue reading “How to improve your writing skills”