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Proteins shape analyses reveal novel forms and connections.

Dr. Muniba Faiza

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Protein shape analyses reveal novel forms and connections.

A new study has revealed new forms of proteins that have never been seen before along with unexpected connections. Last year, Google DeepMind predicted the structure of all known proteins from organisms using AlphaFold [1].

This time researchers mined a database full of the structures of every known protein predicted using AlphaFold neural networks [1]. This database consists of over 200 million protein structures. They have found completely novel shapes and connections between the structures.

A team co-led by Steinegger and computational biologist Pedro Beltrao, at ETH Zurich in Switzerland has developed a tool that can easily compare structures in the database based on their similarities and shapes. This tool is based on a structure alignment clustering algorithm- Foldseek cluster—that can cluster hundreds of millions of structures [2]. It can cluster millions of structures quickly.

This led to the identification of a novel link, as stated by  Steinegger, among different proteins. A protein that humans and other complex organisms use to trigger an immune attack and to detect viral DNA was found in a cluster with proteins from single-celled bacteria and archaea.

Another study done at the University of Basel in Switzerland and the SIB Swiss Institute of Bioinformatics reveals a novel protein shape [3]. The researchers called it a ‘Beta-flower’ as the structures contain hairpin turns which are found in a known protein shape called a Beta-barrel that resembles petals on a flower [4]. According to computational biologist Joana Pereira, proteins that contain Beta-flowers are distantly related to one another, but their function is unclear.


References

  1. Jumper, J., Evans, R., Pritzel, A., Green, T., Figurnov, M., Tunyasuvunakool, K., … & Hassabis, D. (2020). AlphaFold 2. Fourteenth Critical Assessment of Techniques for Protein Structure Prediction; DeepMind: London, UK.
  2. Barrio-Hernandez, I., Yeo, J., Jänes, J. et al., (2023). Clustering-predicted structures at the scale of the known protein universe. Nature.
  3. Durairaj, J., Waterhouse, A.M., Mets, T. et al. (2023). Uncovering new families and folds in the natural protein universe. Nature.
  4. https://www.nature.com/articles/d41586-023-02892-z#ref-CR1

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

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Bioinformatics Programming

DockingAnalyzer.py: A New Python script to Identify Ligand Binding in Protein Pockets.

Dr. Muniba Faiza

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DockingAnalyzer.py-A Python script to identify ligand binding in protein pockets.

High-throughput virtual screening (HTVS) is a pivotal technique in drug discovery that screens extensive libraries of compounds to find potential drug candidates. One of the essential tasks in HTVS is to ensure that ligands are binding within the protein’s binding pocket. This task can be particularly challenging when dealing with thousands of docking results. To address this challenge, we present a Python script that automates the analysis of molecular docking results generated by AutoDock Vina [1] using PyMOL [2]. This script calculates the center of mass (COM) for each docked pose, compares it with a reference ligand’s COM, and identifies poses that bind within a specified threshold distance. This process is crucial in mass docking scenarios where confirming ligand binding within the pocket is necessary. (more…)

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Bioinformatics News

VS_Analysis: A Python package to perform post-virtual screening analysis

Dr. Muniba Faiza

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VS_Analysis: A Python package to perform post-virtual screening analysis

Virtual screening (VS) is a crucial aspect of bioinformatics. As you may already know, there are various tools available for this purpose, including both paid and freely accessible options such as Autodock Vina. Conducting virtual screening with Autodock Vina requires less effort than analyzing its results. However, the analysis process can be challenging due to the large number of output files generated. To address this, we offer a comprehensive Python package designed to automate the analysis of virtual screening results.

(more…)

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Bioinformatics News

What is MANE project?

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What is mane project?

MANE is a collaborative project between NCBI and EMBL-EBI. It stands for Matched Annotation from NCBI and EMBL-EBI [1]. The datasets provided by NCBI and EMBL-EBI on the human genome are not identical across every gene.

(more…)

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This Month in Bioinformatics- Research Updates of March 2022

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This Month in Bioinformatics- Research Updates of March 2022

Here are the latest research developments in the field of bioinformatics made in the month of March 2022. (more…)

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This month in Bioinformatics- Research Updates of November 2021

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This month in Bioinformatics- Research Updates of November 2021

We summarize the latest research published this month in the field of bioinformatics. (more…)

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This Month in Bioinformatics- Research Updates of October 2021

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BLAST+ 2.12.0- A more efficient version of BLAST is available

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BLAST+ 2.12.0- New version

A new more efficient version of BLAST+ 2.12.o is available now [1]. This version provides more efficient multithreaded searches. (more…)

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This Month in Bioinformatics- Research Updates of June 2021

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This Month in Bioinformatics- Research Updates of June 2021

In this article, we summarize the latest interesting findings made this month of June in bioinformatics. (more…)

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This Month in Bioinformatics- Research Updates of May 2021

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This Month in Bioinformatics- Research Updates of May 2021

In this article, we summarize the latest interesting findings made this month in bioinformatics. (more…)

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This Month in Bioinformatics- Research Updates of April 2021

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This Month in Bioinformatics- Research Updates of April 2021

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This Month in Bioinformatics- Research Updates of March 2021

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This Month in Bioinformatics- Research Updates of February 2021

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We summarize the research done in bioinformatics in the month of February. (more…)

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This Month in Bioinformatics- Research Updates of January 2021

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This month in Bioinformatics- January 2021

In this article, we summarize the main findings made in bioinformatics this month. (more…)

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This Month in Bioinformatics- Research Updates of December 2020

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This Month in Bioinformatics- Research Updates of December 2020

In this article, we summarize the latest research in bioinformatics published this month. (more…)

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Join Bioinformatics Review Research Group

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We are going to lead a few bioinformatics research projects. For that, we are creating a new research group of Bioinformatics Review. (more…)

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This Month in Bioinformatics- Research Updates of November 2020

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Research updates of bioinformatics- November 2020

In this article, we summarize the latest research in bioinformatics published this month. (more…)

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This Month in Bioinformatics- Research Updates of October 2020

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monthly-october updates bioinformatics

Some of the important findings made this month in bioinformatics are mentioned in this article. (more…)

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This Month in Bioinformatics: Research Updates of September 2020

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Some of the important findings made this month in bioinformatics are mentioned in this article. (more…)

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This Month in Bioinformatics: Research Updates of August 2020

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