PRESS-NEWS.org - Press Release Distribution
PRESS RELEASES DISTRIBUTION

USC researchers develop AI model that predicts the accuracy of protein–DNA binding

2024-08-08
(Press-News.org) A new artificial intelligence model developed by USC researchers and published in Nature Methods can predict how different proteins may bind to DNA with accuracy across different types of protein, a technological advance that promises to reduce the time required to develop new drugs and other medical treatments.

The tool, called Deep Predictor of Binding Specificity (DeepPBS), is a geometric deep learning model designed to predict protein–DNA binding specificity from protein–DNA complex structures. DeepPBS allows scientists and researchers to input the data structure of a protein–DNA complex into an online computational tool.

“Structures of protein–DNA complexes contain proteins that are usually bound to a single DNA sequence. For understanding gene regulation, it is important to have access to the binding specificity of a protein to any DNA sequence or region of the genome,” said Remo Rohs, professor and founding chair in the department of Quantitative and Computational Biology at the USC Dornsife College of Letters, Arts and Sciences. “DeepPBS is an AI tool that replaces the need for high-throughput sequencing or structural biology experiments to reveal protein–DNA binding specificity.”

AI analyzes, predicts protein–DNA structures

DeepPBS employs a geometric deep learning model, a type of machine-learning approach that analyzes data using geometric structures. The AI tool was designed to capture the chemical properties and geometric contexts of protein–DNA to predict binding specificity.

Using this data, DeepPBS produces spatial graphs that illustrate protein structure and the relationship between protein and DNA representations. DeepPBS can also predict binding specificity across various protein families, unlike many existing methods that are limited to one family of proteins.

“It is important for researchers to have a method available that works universally for all proteins and is not restricted to a well-studied protein family. This approach allows us also to design new proteins,” Rohs said.

Major advance in protein-structure prediction

The field of protein-structure prediction has advanced rapidly since the advent of DeepMind’s AlphaFold, which can predict protein structure from sequence. These tools have led to an increase in structural data available to scientists and researchers for analysis. DeepPBS works in conjunction with structure prediction methods for predicting specificity for proteins without available experimental structures.

Rohs said the applications of DeepPBS are numerous. This new research method may lead to accelerating the design of new drugs and treatments for specific mutations in cancer cells, as well as lead to new discoveries in synthetic biology and applications in RNA research.

About the study: In addition to Rohs, other study authors include Raktim Mitra of USC; Jinsen Li of USC; Jared Sagendorf of University of California, San Francisco; Yibei Jiang of USC; Ari Cohen of USC; and Tsu-Pei Chiu of USC; as well as Cameron Glasscock of the University of Washington.

This research was primarily supported by NIH grant R35GM130376.

###

END


ELSE PRESS RELEASES FROM THIS DATE:

Increasing solid-state electrolyte conductivity and stability using helical structure

Increasing solid-state electrolyte conductivity and stability using helical structure
2024-08-08
Solid-state electrolytes have been explored for decades for use in energy storage systems and in the pursuit of solid-state batteries. These materials are safer alternatives to the traditional liquid electrolyte—a solution that allows ions to move within the cell—used in batteries today. However, new concepts are needed to push the performance of current solid polymer electrolytes to be viable for next generation materials. Materials science and engineering researchers at the University of Illinois Urbana-Champaign have explored the role of helical secondary structure on the conductivity of solid-state peptide polymer ...

The threat of mpox has returned, but public knowledge about it has declined

The threat of mpox has returned, but public knowledge about it has declined
2024-08-08
PHILADELPHIA – It has been two years since the World Health Organization declared a global health emergency over an outbreak of mpox, a disease endemic to Africa that had spread to scores of countries. Now, in the summer of 2024, a deadlier version of the infectious disease has spread from the Democratic Republic of Congo to other African nations, the strain that originally hit the United States has shown signs of a resurgence, and this week the Centers for Disease Control and Prevention (CDC) issued a new alert on mpox to health care providers. But while the American public quickly learned about the disease during the summer of 2022, as ...

How does traumatic brain injury progress to Alzheimer’s disease?

2024-08-08
RIVERSIDE, Calif. -- A traumatic brain injury, or TBI, is caused by a contusion to the head that may result in injury to the brain. This type of injury combined with the inherited genetic risk factors can result in the accelerated development of Alzheimer’s disease and related dementia, or ADRD. TBIs range from mild to severe, with the majority being mild. They are especially common in adolescents engaging in contact sports and in the elderly who tend to fall with greater frequency as they age. Regardless of the source, TBI and how it progresses to ADRD is an understudied area of research. A $3.5 million grant to the University of California, ...

Researchers find unexpectedly large methane source in overlooked landscape

Researchers find unexpectedly large methane source in overlooked landscape
2024-08-08
When Katey Walter Anthony heard rumors of methane, a potent greenhouse gas, ballooning under the lawns of fellow Fairbanks residents, she nearly didn’t believe it. “I ignored it for years because I thought ‘I am a limnologist, methane is in lakes,’” she said. But when a local reporter contacted Walter Anthony, who is a research professor at the Institute of Northern Engineering at University of Alaska Fairbanks, to inspect the waterbed-like ground at a nearby golf course, she started to pay attention. Like others in Fairbanks, they lit “turf bubbles” on fire and confirmed the presence of methane ...

Royal Commission for AlUla collaborates with SETI Institute to support development of Alula Manara Observatory

Royal Commission for AlUla collaborates with SETI Institute to support development of Alula Manara Observatory
2024-08-08
Royal Commission for AlUla Collaborates with SETI Institute to Support Development of AlUla Manara Observatory   Experts from SETI Institute will support the advancement of telescope technology and data analysis at AlUla Manara Observatory.  The collaboration will enhance the future observatory's capabilities as it welcomes global scientists, researchers, and tourists interested in astronomy and space science. Ambitions to foster curiosity, knowledge sharing, and upskilling local capabilities in astronomical and space sciences field Mountain View, CA , 8 August 2024 -- The Royal Commission for AlUla (RCU) and SETI Institute ...

Cutting a few calories won’t hurt your workout

Cutting a few calories won’t hurt your workout
2024-08-08
A new UC Riverside study demonstrates that calorie restriction doesn’t deter mice from exercising, challenging the belief that dieting drains workout energy. The study, published in the journal Physiology & Behavior, shows that cutting calories by 20% did not significantly reduce the distance that mice voluntarily chose to run each day.  The researchers set out to understand what happens to mice when the amount of food available to them is reduced.  The findings, they hoped, would be relevant ...

Study reveals ways in which 40Hz sensory stimulation may preserve brain’s ‘white matter’

Study reveals ways in which 40Hz sensory stimulation may preserve brain’s ‘white matter’
2024-08-08
Early-stage trials in Alzheimer’s disease patients and studies in mouse models of the disease have suggested positive impacts on pathology and symptoms from exposure to light and sound presented at the “gamma” band frequency of 40 Hz. A new study zeroes in on how 40Hz sensory stimulation helps to sustain an essential process in which the signal-sending branches of neurons, called axons, are wrapped in a fatty insulation called myelin. Often called the brain’s “white matter,” myelin protects axons and insures better ...

Record-breaking recovery of rocks that originated in Earth’s mantle could reveal secrets of planet’s history

Record-breaking recovery of rocks that originated in Earth’s mantle could reveal secrets of planet’s history
2024-08-08
Scientists have recovered the first long section of rocks that originated in the Earth’s mantle, the layer below the crust and the planet’s largest component. The rocks will help unravel the mantle’s role in the origins of life on Earth, the volcanic activity generated when it melts, and how it drives the global cycles of important elements such as carbon and hydrogen, according to the team. The nearly continuous 1,268 metres of mantle rock was recovered from a “tectonic window,” a section ...

Surprise: infected bacteria fight back with “hidden” genes that halt cell growth, slow viral spread

2024-08-08
Researchers have uncovered a surprising way bacteria defend themselves: when a bacterium is infected, bacterial enzymes that copy genetic information from RNA into DNA synthesize genes whose protein products help shut down cell growth. This prevents further viral spread in the neighboring bacterial population. The results highlight the potential for other “hidden” genes, like the one found here, to be unearthed in different biological contexts. Bacteria defend themselves from viral ...

Early prenatal exposure to famine increases Type 2 diabetes risk in adulthood, shows study of historical Ukraine event

2024-08-08
Prenatal exposure to famine significantly increases the risk of developing Type 2 diabetes mellitus (T2DM) in adulthood, according to a new study of people impacted by the 1932-1933 Holodomor famine in Ukraine. While the immediate and short-term effects of famines on mortality and morbidity are well-documented, deciphering famines’ long-term health consequences – as this study did – has been more difficult. Previous research has suggested a link between prenatal nutrition and adult health ...

LAST 30 PRESS RELEASES:

Reality check: making indoor smartphone-based augmented reality work

Overthinking what you said? It’s your ‘lizard brain’ talking to newer, advanced parts of your brain

Black men — including transit workers — are targets for aggression on public transportation, study shows

Troubling spike in severe pregnancy-related complications for all ages in Illinois

Alcohol use identified by UTHealth Houston researchers as most common predictor of escalated cannabis vaping among youths in Texas

Need a landing pad for helicopter parenting? Frame tasks as learning

New MUSC Hollings Cancer Center research shows how Golgi stress affects T-cells' tumor-fighting ability

#16to365: New resources for year-round activism to end gender-based violence and strengthen bodily autonomy for all

Earliest fish-trapping facility in Central America discovered in Maya lowlands

São Paulo to host School on Disordered Systems

New insights into sleep uncover key mechanisms related to cognitive function

USC announces strategic collaboration with Autobahn Labs to accelerate drug discovery

Detroit health professionals urge the community to act and address the dangers of antimicrobial resistance

3D-printing advance mitigates three defects simultaneously for failure-free metal parts 

Ancient hot water on Mars points to habitable past: Curtin study

In Patagonia, more snow could protect glaciers from melt — but only if we curb greenhouse gas emissions soon

Simplicity is key to understanding and achieving goals

Caste differentiation in ants

Nutrition that aligns with guidelines during pregnancy may be associated with better infant growth outcomes, NIH study finds

New technology points to unexpected uses for snoRNA

Racial and ethnic variation in survival in early-onset colorectal cancer

Disparities by race and urbanicity in online health care facility reviews

Exploring factors affecting workers' acquisition of exercise habits using machine learning approaches

Nano-patterned copper oxide sensor for ultra-low hydrogen detection

Maintaining bridge safer; Digital sensing-based monitoring system

A novel approach for the composition design of high-entropy fluorite oxides with low thermal conductivity

A groundbreaking new approach to treating chronic abdominal pain

ECOG-ACRIN appoints seven researchers to scientific committee leadership positions

New model of neuronal circuit provides insight on eye movement

Cooking up a breakthrough: Penn engineers refine lipid nanoparticles for better mRNA therapies

[Press-News.org] USC researchers develop AI model that predicts the accuracy of protein–DNA binding