In this article, we are going to download FASTA sequences for multiple structures from PDB . We need to have PDB IDs only for input.
You can download FASTA sequences as separate files or in a single file for multiple structures in PDB. Follow these steps:
- Go to https://www.rcsb.org/downloads/fasta
- Select an appropriate option from the left whether you want to enter PDB IDs or Entity IDs or assembly IDs
- Enter IDs separated by a comma.
- Select from the right whether you want to download individual FASTA files or a single FASTA file for all.
- Click ‘Launch Download’.
Common mistakes made during computational docking.
Computational docking is not a trivial task once we avoid making some mistakes. In this section, let’s learn about some important points that we should keep in mind while performing computational docking.
How to install the LigAlign plugin on Pymol on Ubuntu (Linux)?
Few errors appear when we try to run the LigAlign plugin  in Pymol . For example, if you try to run the ligand_alignment plugin, it will give you multiple errors including “Unable to initialize LigAlign v1.00“, or “can’t run LigAlign v1.00” or “incorrect Python syntax” or “Plugin has been installed but initialization failed“. In this article, we explain the reason for this issue and how you can rectify these errors. (more…)
How to make an impactful science presentation?
After your hard work, it is time to showcase your study and the methods of your study to an audience. You must make every point useful and informative. Here, in this article, we are going to share some tips to make your scientific presentation impactful. (more…)
Basic bioinformatics concepts to learn for beginners
A Beginner’s Guide on How to Write Good Manuscripts
Drafting a manuscript could be a difficult task for beginners in the field of research. In this article, we will provide a few tips for how can you write a good manuscript being a research scholar. (more…)
How to remove HETATMS and chains from PDB file?
Importance of Reasoning in Research
Research is considered complicated. As it involves reading multiple research articles and reviews, devising hypotheses and appropriate experiments, and last but not the least, getting a significant output. This seems difficult to read multiple research papers and then extract useful information regarding your project. It involves a methodology to read and understand research articles in one go. This is explained in our previous article “A guide on how to read the research articles”. This article explains the importance of thinking during your entire research. (more…)
How to Find Binding Pocket/ Binding Site for Docking?
Finding binding sites/pockets in a target protein is one of the important steps in docking studies. It is relatively easier to find a binding pocket in the proteins whose resolved structures are available in PDB than that of the predicted structures. In this article, we will discuss the ways to know a binding pocket or a binding site in a target protein. (more…)
Careers in Bioinformatics and Computational Biology
Current Research Topics in Bioinformatics
Researchers working in the scientific area always want to explore new and hot topics to make informed choices. In this article, all new, current, and demanding research topics in bioinformatics are mentioned. This article is helpful for the researchers who are looking for trends in bioinformatics to select a research topic of broad-spectrum. (more…)
MD Simulation using GROMACS: Things to remember
Molecular dynamics (MD) simulation is considered amongst the important methods in bioinformatics. Installation of MD simulation software and execution of their commands is critical. It requires several parameters to be considered before performing simulations. A single mistake may result in impractical outputs. In this article, we will discuss such important things to remember during the MD simulation and installation and execution of its software (GROMACS) [1,2]. (more…)
List of Bioinformatics Books for Beginners
Bioinformatics- Where & How to Start?
Bioinformatics being an interdisciplinary area of biological science and computer science may sound complicated to beginners in this field. However, it is quite simple. The only thing you need is knowledge in both areas. Here is a way for the beginners to start with bioinformatics. (more…)
Common mistakes made during Autodock Vina Installation and Execution
Several errors occur while installing MGLTools and Autodock Vina on Ubuntu. We have explained the complete process of Autodock Vina installation and docking in previous articles. Here are some common errors and mistakes that should be taken care of while installing and running Vina on Ubuntu. (more…)
What does a bioinformatician do?
Bioinformaticians play an important part in data analysis and result interpretation in the field of bioinformatics. However, it is unclear to many what specific role bioinformaticians play day to day. We are often asked by many about what exactly a bioinformatician does. But first, who is a bioinformatician?
MGL Tools & Autodock Vina installation: Frequently Asked Questions and Answers
I have received several e-mails from researchers and students alike regarding installing MGL Tools and Autodock Vina on Ubuntu. Most questions are similar in nature, so I thought of answering them once and for all. In this article, I have collected some frequently asked questions and provided the link to their answers in our question-answer section of Bioinformatics Review. (more…)
A guide on how to read the research articles
Reading 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. (more…)
Bioinformatics and programming languages- what do you need to know!
There are various things which come to mind when someone is going to enter in the field of Bioinformatics and the topmost concern is “Do I need to learn computer languages to pursue my career in Bioinformatics?”. The answer is a bit tricky but it could be both “yes” and “no”. This article will describe the conditions where you need to learn programming languages in Bioinformatics. (more…)
Site-specific docking: Frequently Asked Questions & answers for starters
I have been getting several E-mails from researchers and students alike regarding in-silico docking. Most questions are similar in nature, so I thought of answering them once and for all. In this article, I have collected some frequently asked questions and provided the link to their answers present in our question-answer section of Bioinformatics Review.
It is good to have questions in mind and they can be solved in a way as quoted by Sir Einstein:
“We cannot solve our problems with the same thinking we used when we created them.”
In this article, I have collected some of the most Frequently Asked Questions while performing site-specific and/ or blind docking. You have to consider a lot of factors before performing an actual docking on a protein with a specific ligand.
Question: I have to find the 4 Armstrong neighborhood of a ligand. When I take the receptor molecule without adding hydrogen bonds and find 4A nbd of ligand, it gives one result. But when I first add hydrogens to the receptor molecule and then after finding the 4A nbd of ligand, it obviously gives different results. I want to know which one is better ??
Survival guide: How to overcome lab politics and not become a lab rat
If you find yourself in a laboratory full of people with scientific temperament, it can be exciting, awesome and hilarious. You may experience a real life “big bang theory” episode and witness all characters around you.
However, for the uninitiated, a large number of labs are a flourishing ground of rivalry and war grounds reiterating the fact on its inhabitant that they live in a maze.
Lab politics can be nasty, and those who don’t want to get involved are almost certainly the easiest target.
Here are a few tips based on my experience in labs on how to survive lab politics and prevent yourself from getting into situations uncalled for.
- Communicate Backbiting and misinformation is the nuclear weapon of every mole. They pass on false information about you leading to complexities. It ranges from simple misinformation about you being absent or drunk during work hours when you are not, to some complicated statements attributed to you. You can deal with this situation through regular communication. with your peers. Every one of them. Especially if you sense that your guide is growing weary of you. communicate as clearly as possible and if you sense misinformation, make it a priority to point it out without targeting the person acting as a mole. This will be such a blow…..oops!
- Be Humble
Back in my graduation days, I was made a leader for a group project, I worked harder than everybody suddenly realizes that it was only me that was working for the whole duration. So I became proud which reflected in my behavior. Seeing this, two girls approached the guide with some story, which I am still unaware of. The guide, who happens to be a lady, immediately removed me from the project & my name from the manuscript after it completed. The results were published without my name, the first author being that girl who was not even fully aware of the topic. Moral? even if you are doing everything, be humble or you risk being a lab rat.
- Divert to productivity
When somebody else is the target, it is relatively easy for you to just ignore what is happening but remaining silent in such situations will lead to an exponential increase in it and you never know when the dial points at you. You may try shifting focus to an interesting observation, experiment, or paper. This way, you show them that what these guys are talking about is not worth the time.
- Don’t be evil If someone is doing something a certain way and you know they are wrong, just point it to them. Don’t go to your guide to complain. If you complain too much it is perceived as a negative trait. If you have problems try to resolve them on your own rather than asking someone to do them for you. If you can’t do it yourself, try to get help rather than ordering. Nobody owes you anything so be humble.
- Don’t over-promise
You may become a target without even saying a word! yes! it happens. The world is full of hatred for achievers. So if you have a lot in your kitty, don’t keep flaunting it. don’t promise that you will do this and that. Just keep doing things one by one. So they won’t even notice that you were running your own race and they were not even the participants.
6. Don’t get discouraged
If you are surrounded by ‘lab politicians’ and they criticize your work and working habits, then don’t get discouraged, because they would be trying to distract you from your work. In fact, it is a good sign, great success comes with criticism. Don’t believe what they say because ‘politicians’ never want anyone else’s account to be filled, just say thanks to them with a smile and keep going in your direction.
These are the tips that I have learned by working at labs in the University of Delhi, Indian Institute of Science Education & Research – Kolkata, Jamia Millia Islamia & Jawaharlal Nehru University.
Although I have tried to accommodate as much as I could, do you think I have missed something? would like to add something to the story? go ahead and comment below.