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How to download FASTA sequences from PDB for multiple structures?

Dr. Muniba Faiza

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How to download FASTA sequences from PDB for multiple structures?

In this article, we are going to download FASTA sequences for multiple structures from PDB [1]. 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’.

References

  1. https://www.rcsb.org

Dr. Muniba is a Bioinformatician based in New Delhi, India. She has completed her PhD in Bioinformatics from South China University of Technology, Guangzhou, China. She has cutting edge knowledge of bioinformatics tools, algorithms, and drug designing. When she is not reading she is found enjoying with the family. Know more about Muniba

Software

CMake installation and upgrade: What worked & what didn’t?!

Dr. Muniba Faiza

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CMake installation and upgrade: What worked & what didn’t?!

CMake is a widely used cross-platform build system that automates the process of compiling and linking software projects. In bioinformatics, CMake can be utilized to manage the build process of software tools and pipelines used for data analysis, algorithm implementation, and other computational tasks. However, managing the versions of CMake or upgrading it on Ubuntu (Linux) can be a trivial task for beginners. In this article, we provide methods for installing and upgrading CMake on Ubuntu.

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Tips & Tricks

Common mistakes made during computational docking.

Dr. Muniba Faiza

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Common mistakes made during 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.

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Software

How to install the LigAlign plugin on Pymol on Ubuntu (Linux)?

Dr. Muniba Faiza

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How to install the LigAlign plugin on Pymol on Ubuntu (Linux)?

Few errors appear when we try to run the LigAlign plugin [1] in Pymol [2]. 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…)

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Tips & Tricks

How to make an impactful science presentation?

Dr. Muniba Faiza

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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…)

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Tips & Tricks

Basic bioinformatics concepts to learn for beginners

Dr. Muniba Faiza

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Basic Concepts in Biology & Bioinformatics for Beginners

This article is for beginners who are stepping into the field of bioinformatics. We will discuss some basic concepts that you need to learn while trying to enter the field of bioinformatics. (more…)

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Tips & Tricks

A Beginner’s Guide on How to Write Good Manuscripts

Dr. Muniba Faiza

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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…)

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Tips & Tricks

How to remove HETATMS and chains from PDB file?

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Removing HETATM and chains from pdb files

This is a basic tutorial on removing the hetero-atoms (HETATMS) and chains from PDB files. It is an essential step for computational and molecular dynamics simulation. (more…)

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Tips & Tricks

Importance of Reasoning in Research

Dr. Muniba Faiza

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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…)

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Docking

How to Find Binding Pocket/ Binding Site for Docking?

Dr. Muniba Faiza

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Finding binding pocket in target protein

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…)

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Tips & Tricks

Careers in Bioinformatics and Computational Biology

Dr. Muniba Faiza

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careers in bioinformatics

Bioinformatics is an interesting field of research combining biological sciences and computer sciences. In this article, we will discuss making careers in bioinformatics for starters. (more…)

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Tips & Tricks

Current Research Topics in Bioinformatics

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hot 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…)

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MD Simulation

MD Simulation using GROMACS: Things to remember

Dr. Muniba Faiza

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MD Simulation

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…)

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Bioinformatics Books

List of Bioinformatics Books for Beginners

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List of Bioinformatics books for beginners

It is difficult to decide which book to read to start learning bioinformatics. Beginners can read this article to know the basic steps involved in learning bioinformatics. A few books are suggested in this article to read for starters in bioinformatics. (more…)

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Tips & Tricks

Bioinformatics- Where & How to Start?

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How to start with Bioinformatics

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…)

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Docking

Common mistakes made during Autodock Vina Installation and Execution

Dr. Muniba Faiza

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mistakes & errors 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…)

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Tips & Tricks

What does a bioinformatician do?

Dr. Muniba Faiza

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What bioinformaticians 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?

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Software

MGL Tools & Autodock Vina installation: Frequently Asked Questions and Answers

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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…)

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Tips & Tricks

A guide on how to read the research articles

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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…)

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Tips & Tricks

Bioinformatics and programming languages- what do you need to know!

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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…)

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Docking

Site-specific docking: Frequently Asked Questions & answers for starters

Dr. Muniba Faiza

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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: How do you predict protein’s binding sites? 

Question:  What is the difference between the blind docking and binding site based docking?

  
 
 
Second thing, if I have to find the distance between a ligand and any residue in the receptor molecule. Do I have to take the central atom distances or minimum distance between any two atoms of the ligand and receptor molecule can be considered ?? 
 
   
If these are not the questions you are looking for, then feel free to ask in our ‘Bioinformatics Discussion‘ section or write to [email protected].
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