#computationalbiology

[everythingaboutbiotech]

Looking to enhance your bioinformatics skills and take your research to the next level? Look no further than justbio - your one-stop-shop for all things bioinformatics!

[masterclassofcl]

What is the term used to describe the interdisciplinary field that combines biology and computer science to analyze and interpret biological data?

a) Computational Biology b) Bioinformatics c) Systems Biology d) Biostatistics

[mysticalpeacenut]

Explore Drugs Targeting RNA Riboswitches with Magna - Depixus

We’ve been working with Dr Jay Schneekloth, a leading expert in RNA-targeted drug discovery, to use our MAGNA™ technology to probe the interactions between the PreQ1 bacterial riboswitch and its natural ligand or a synthetic small molecule.

In a paper published as a preprint on bioRxiv and submitted for publication in a high impact journal, we showed how MAGNA provided novel insights into the distinct mechanisms of action of different ligands upon the target RNA at single molecule resolution.

What is the PreQ1 bacterial riboswitch?

Riboswitches are structured sequences of RNA that are commonly found in the 5′ untranslated regions of bacterial mRNAs and help to control metabolic pathways. They work through direct binding of a ligand such as a metabolite to the riboswitch, which induces a conformation change to their secondary structure and alters gene expression.

The PreQ1 riboswitch regulates downstream gene expression for the biosynthesis of queuosine in response to a metabolite called PreQ1 (7-aminomethyl-7-deazaguanine). Upon binding of PreQ1 the RNA changes into a shape known as a pseudoknot, which alters gene expression at either the transcriptional or translational level.

The ability of riboswitches to modulate bacterial gene expression in response to small molecules such as metabolites makes them an attractive group of novel antibacterial drug targets.

Using MAGNA to explore RNA-ligand interactions

Based on magnetic force spectroscopy, MAGNA is the first technology for exploring dynamic molecular interactions in real time from up to thousands of individual molecules. Here, we used it to probe the interactions between the PreQ1 riboswitch RNA from Bacillus subtilis (Bsu) and its natural ligand, PreQ1, or a synthetic ligand named Compound 4.

MAGNA allows us to precisely measure the effects of applying constant or gradually changing (ramped) forces to hundreds of immobilized riboswitch RNAs simultaneously (Figure 1A). This enabled us to capture the exact point at which each RNA molecule changes conformation.

We found that both PreQ1 and Compound 4 stabilized the riboswitch RNA structure, requiring more force to unfold it (Figure 1B). We were also able to explore the concentration dependency of their effects (Figure 1C, E, F).

Figure 1: (A) Overview of MAGNA as a single-molecule platform for exploring the interactions of bioactive small molecule ligands with their target RNA structures in real-time (B) Unfolding force distributions of the Bsu PreQ1 riboswitch aptamer in control (DMSO), Compound 4 and PreQ1 ligand conditions (C) Dose-response curve for the change in unfolding of the aptamer in the presence of 4 and PreQ1 (D) Raw traces of the constant-force experiments for control, 4 and PreQ1 of a single molecule with cumulative density histograms shown to the right. (E) The aptamer unfolding rate as a function of the concentration of 4 in constant force experiments. (F) The impact of PreQ1 ligand concentration on the occurrence probability of the stable folded state. n is the number of molecules analyzed. Taken from Parmar et al (bioRxiv, 2024).

In addition, Schneekloth and colleagues explored other structural aspects of the interaction between the riboswitch and various ligands, and their impact on gene expression in live bacterial cells. They were also able to show that Compound 4 could bind in a similar way to PreQ1 riboswitches from other species of bacteria, building up a fuller picture of the properties of this novel molecule.

Deeper insights for RNA-targeted drug development

Overall, the findings presented in the paper demonstrate that even though different ligands may appear to be the same in terms of RNA binding site and impact on gene expression, other factors including selectivity, mode of recognition, and impacts on both conformational kinetics and thermodynamics, can all play

 a role in the abili

ty of a compound to modulate biological function. These subtle yet important distinctions may not be apparent using analytical methods that rely on surrogate outputs or bulk measurements.

MAGNA’s unique single molecule approach enabled the Schneekloth team to visualize the binding of a novel ligand to its target in real time and gather insights into the distinct mechanisms of action, which would not have been possible using other methods.

With MAGNA we now have a technology that can not only identify compounds that bind to RNA, but also directly reveal how they impact its structure and function at the level of individual molecules. And we can use it to generate detailed information about the kinetics and concentration dependence of ligand binding.

These results demonstrate the capabilities of MAGNA to deliver valuable data about individual dynamic molecular interactions at scale, supporting lead selection in the development of novel RNA-targeted therapeutics.

Read More here: https://depixus.com/using-magna-to-explore-drugs-targeting-rna-riboswitches/  

[r0man-sanchez]

The New Human Project

Our Purpose Here at Novena we have one goal: to preserve the history of human achievement through science and technology. We are dedicated to ensuring that our knowledge and wisdom continues to live long after we have gone extinct, long after our planet has died, long after our star has disappeared. Death is an inevitability, but by working together with the latest giant in today’s leading…

[karkidi-data-science-jobs]

How do I get a job in computational biology?

In the career path of this field, you can either take bioscience or any other branch of life science or computer science and engineering at the undergrad level.

One must be fluent in understanding life science terminology of genetics, genomics, and cellular biology.

[jobrxiv]

Postdoctoral Fellow in Computational Genomics UMass Chan Medical School Come join the Abdennur Lab (https://abdenlab.org/) as a #postdoc in #Genomics and #ComputationalBiology at @UMassChan! See the full job description on jobRxiv: https://jobrxiv.org/job/umass-chan-medical-school-27778-postdoctoral-fellow-in-computational-genomics/?feed_id=72215 #3d_genomics #artificial_intelligence #computational_biology #data_science #functional_genomics #ScienceJobs #hiring #research

[labis-unicamp]

Don't pass up the chance to take part in the most important conference for those interested in bioinformatics and computational biology in Latin America! The next X-Meeting / BSB 2023 will include outstanding seminars, workshops, poster presentations, and much, much more. Get to know some of the most knowledgeable people in your field and broaden your professional network. Register today and make sure you don't miss out on this chance to gain new knowledge, interact with others, and be inspired! Visit https://4et.us/xm23 #XMeeting2023 #Bioinformatics #ComputationalBiology

[ab3c]

Don't pass up the chance to take part in the most important conference for those interested in bioinformatics and computational biology in Latin America! The next X-Meeting / BSB 2023 will include outstanding seminars, workshops, poster presentations, and much, much more. Get to know some of the most knowledgeable people in your field and broaden your professional network. Register today and make sure you don't miss out on this chance to gain new knowledge, interact with others, and be inspired! Visit https://4et.us/xm23 #XMeeting2023 #Bioinformatics #ComputationalBiology

[omicium-blog]

This a beautiful protein called Chimotrypsin, A Pancreatic digestive enzyme, helps in breakdown of proteins. Looks Cool though! Can be taken as an enzyme suppliment and an anti-inflamatory agent. Monomer and polymeric forms. . . . #bioinformatics #science #biology #phd #research #scientist #medicine #lab #bio #computerscience #biochemistry #microbiology #molecularbiology #biotech #biotechnology #phdlife #genetics #datascience #bioinformaticslife #computationalbiology #epidemiology #biologist #microbiologist #biologystudent #biologyteacher #researcher #scientific #biotechnologystudent #researchers #lifesciences https://www.instagram.com/p/CEmJLxWj8I0/?igshid=kusqq8wsjnkp

[scientistdidwhat]

Genetics PhD student appreciates unnecessary, hostile, and misinformed feedback.

PhD student Janet Small has established a reputation as consistently receptive to, “unnecessary, harsh, and ultimately misguided criticism,” beamed her supervisor. Her colleague, Dan, agrees. “She never argues,” added Dan, nodding. “And she’s always smiling. I like that. I wonder if she’s seeing anybody.” Small, who organizes LGBTAQ+ student gatherings, shared that she expects little from her colleagues and supervisor, whom she perceives as self-interested and unimaginative, but wishes them the best. Adding that she always ignores Dan’s advice, she holds the record for departmental doctoral student publications, a fact she shared while smiling.

[sayalibhokare]

Computational Biology Market to Grow at 13.6 by 2028: COVID Impact & Post COVID Analysis, Business Opportunities, and Strategies

In 2018, the global computational biology market was valued at USD 2.9 billion, with a CAGR of 21.5 percent predicted over the forecast year. Growing drug discovery R&D, demand for predictive models, use in population-based sequencing efforts like the human genome project, and government financing are all driving the market forward. For example, in March 2019, Ambrx Inc., a clinical-stage biopharmaceutical business specializing in protein therapies, struck a research and development agreement with BeiGene, Ltd., a commercial-stage pharmaceutical company.

According to a new analysis, the global computational biology market is estimated to reach USD 13.6 billion by 2026. During the forecast period, it is expected to grow at a CAGR of 21.3 percent.

read more @ https://bhaokresayali.blogspot.com/2021/08/computational-biology-market-to-grow-at.html

[mysticalpeacenut]

How MAGNA™ Technology is Revolutionizing the Study of Biomolecular Interactions

In the world of science, understanding how molecules interact with each other is crucial for developing new drugs, diagnostics, and other life-saving technologies. However, traditional methods for studying these interactions are often time-consuming, expensive, and inaccurate.

MAGNA™ technology is a new and innovative approach that is revolutionizing the way we study biomolecular interactions. This powerful tool can measure the strength, structure, and location of interactions between molecules with unprecedented precision and sensitivity.

What is MAGNA™ technology?

MAGNA™ technology is based on a novel method called bioluminescence resonance energy transfer (BRET), It is developed by Depixux. BRET uses light to measure the distance between two molecules. When two molecules that are labeled with special BRET tags come close together, they can transfer energy from one to the other, which produces a light signal. The intensity of the light signal is proportional to the distance between the molecules.

How does MAGNA™ technology work?

MAGNA™ technology can be used in three different modes:

Binding strength mode: In this mode, MAGNA™ is used to measure the force required to pull apart two molecules. This can be used to study the strength of drug-target interactions, protein-protein interactions, and other biomolecular interactions.

Binding structure mode: In this mode, MAGNA™ is used to measure the effect of another molecule on the structure of a target molecule. This can be used to study how drugs bind to their targets, how proteins interact with each other, and how other molecules can alter the structure of biomolecules.

Binding location mode: In this mode, MAGNA™ is used to measure the precise location on a molecule where another molecule binds. This can be used to study the binding sites of drugs, the active sites of enzymes, and other important regions of biomolecules.

What are the benefits of MAGNA™ technology?

MAGNA™ technology offers several advantages over traditional methods for studying biomolecular interactions:

High sensitivity: MAGNA™ can detect interactions between molecules that are too weak to be measured by other methods.

High precision: MAGNA™ can measure the distance between molecules with high accuracy.

Real-time: MAGNA™ can measure interactions in real time, which allows researchers to study the dynamics of biomolecular interactions.

Label-free: MAGNA™ does not require the molecules to be labeled with special tags, which can simplify experiments and reduce costs.

How is MAGNA™ technology being used?

MAGNA™ technology is being used in a variety of research applications, including:

Drug discovery: MAGNA™ is being used to identify new drug targets and to develop new drugs that are more effective and have fewer side effects.

Diagnostics: MAGNA™ is being used to develop new diagnostic tests for diseases such as cancer and Alzheimer's disease.

Protein engineering: MAGNA™ is being used to engineer proteins with new properties and functions.

The future of MAGNA™ technology

MAGNA™ technology is a powerful tool that is revolutionizing the way we study biomolecular interactions. This technology has the potential to lead to the development of new drugs, diagnostics, and other life-saving technologies. As MAGNA™ technology continues to develop by Depixus, we can expect to see even more exciting discoveries in the years to come.

[biodiscovery-group]

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[sachincmi]

What is Computational Biology? Why it has become important part of genomics, drug discovery, and other biomedical applications?

In recent years, Computational Biology has become an integral part of the life sciences. Since the mid-1990s, a group of research teams in various disciplines of science and medicine has been making use of mathematical algorithms to discover new solutions to biological problems. Today, this has become a very effective way for scientists to solve challenging problems. This method has been used by scientists in various fields like genomics, drug discovery, and other biomedical applications. Computational biology is an interdisciplinary discipline that develops software and algorithms for the analysis and interpretation of biological data, especially when the data is very large and complicated.

The field of Computational Biology involves developing methods that are able to find answers to questions regarding biological processes and systems, from the simplest cells to large-scale ecosystems. This is possible because the tools available are designed to use the most advanced techniques and software to make it much more efficient. This type of research is used in various areas, but one of the most popular areas is to help scientists discover solutions to complex medical and societal issues.

Read more @ https://coherentmarketinsights-cmi.blogspot.com/2020/12/what-is-computational-biology-why-it.html