(Press-News.org) WASHINGTON, August 29, 2023 – With their intricate arrangements and dynamic functionalities, proteins perform a plethora of biological tasks by employing unique arrangements of simple building blocks where geometry is key. Translating this nearly limitless library of arrangements into their respective functions could let researchers design custom proteins for specific uses.
In Journal of Applied Physics, from AIP Publishing, Markus Buehler of the Massachusetts Institute of Technology combined attention neural networks, often referred to as transformers, with graph neural networks to better understand and design proteins. The approach couples the strengths of geometric deep learning with those of language models not only to predict existing protein properties but also to envision new proteins that nature has not yet devised.
“With this new method, we can utilize all that nature has invented as a knowledge basis by modeling the underlying principles,” Buehler said. “The model recombines these natural building blocks to achieve new functions and solve these types of tasks.”
Owing to their complex structures, ability to multitask, and tendency to change shape when dissolved, proteins have been notoriously difficult to model. Machine learning has demonstrated the ability to translate the nanoscale forces governing protein behavior into working frameworks describing their function. However, going the other way — turning a desired function into a protein structure — remains a challenge.
To overcome this challenge, Buehler’s model turns numbers, descriptions, tasks, and other elements into symbols for his neural networks to use.
He first trained his model to predict the sequencing, solubility, and amino acid building blocks of different proteins from their functions. He then taught it to get creative and generate brand new structures after receiving initial parameters for a new protein’s function.
The approach allowed him to create solid versions of antimicrobial proteins that previously had to be dissolved in water. In another example, his team took a naturally occurring silk protein and evolved it into various new forms, including giving it a helix shape for more elasticity or a pleated structure for additional toughness.
The model performed many of the central tasks of designing new proteins, but Buehler said the approach can incorporate even more inputs for more tasks, potentially making it even more powerful.
“A big surprise element was that the model performed exceptionally well even though it was developed to be able to solve multiple tasks. This is likely because the model learns more by considering diverse tasks,” he said. “This change means that rather than creating specialized models for specific tasks, researchers can now think broadly in terms of multitask and multimodal models.”
The broad nature of this approach means this model can be applied to many areas outside protein design.
“While our current focus is proteins, this method has vast potential in materials science,” Buehler said. “We're especially keen on exploring material failure behaviors, aiming to design materials with specific failure patterns.”
###
The article “Generative pretrained autoregressive transformer graph neural network applied to the analysis and discovery of novel proteins” is authored by Markus Buehler. It will appear in Journal of Applied Physics on Aug. 29, 2023 (DOI: 10.1063/5.0157367). After that date, it can be accessed at https://doi.org/10.1063/5.0157367.
ABOUT THE JOURNAL
The Journal of Applied Physics is an influential international journal publishing significant new experimental and theoretical results in all areas of applied physics. See https://aip.scitation.org/journal/jap.
###
END
Neural network helps design brand new proteins
A flexible, language-based approach proves surprisingly effective at solving intractable problems in materials science.
2023-08-29
ELSE PRESS RELEASES FROM THIS DATE:
Some hosts have an “evolutionary addiction” to their microbiome
2023-08-29
We’ve long known that hosts malfunction without their microbiome—whether they are missing key microbial species or are completely microbe free. This malfunctioning is usually explained by the need for microbes to perform unique and beneficial functions, but evolutionary ecologist Tobin Hammer of the University of California, Irvine, is questioning that narrative.
In a peer-reviewed opinion article publishing August 29 in the journal Trends in Microbiology, Hammer argues that, in some cases, microbes might not actually be helping their hosts; instead, microbe-free hosts might malfunction because they have evolved an addiction to their microbes. ...
A lightweight wearable device helps users navigate with a tap on the wrist
2023-08-29
Scientists at Rice University in Houston, Texas have developed a fabric-based wearable device that “taps” a user’s wrist with pressurized air, silently helping them navigate to their destination. The study, published August 29 in the journal Device, demonstrated that users correctly interpreted which direction the device was telling them to go an average of 87% of the time. Since the wearable embeds most of its control system within the fabric itself, using air instead of electronics, it can be built lighter and more compact than existing designs.
“We envision this device will be used by individuals who need or desire information to be transmitted ...
Long-term maternal and child outcomes following postnatal SSRI treatment
2023-08-29
About The Study: The results of this study of 61,000 mother-child dyads suggest that postnatal selective serotonin reuptake inhibitor (SSRI) treatment was associated with a reduced risk of postnatal depression–associated maternal mental health problems and child externalizing behaviors across early childhood years. These findings suggest that postnatal SSRI treatment may bring benefits in the long term to women with postnatal depression and their offspring.
Authors: Chaoyu Liu, M.D., Ph.D., of King’s College in London, is the corresponding author.
To access the ...
Cannabis use disorder and reasons for use in a state where recreational cannabis use is legal
2023-08-29
About The Study: In this study of primary care patients in a state with legal recreational cannabis use, cannabis use disorder (CUD) was common among patients who used cannabis. Moderate to severe CUD was more prevalent among patients who reported any nonmedical use. These results underscore the importance of assessing patient cannabis use and CUD symptoms in medical settings.
Authors: Gwen T. Lapham, Ph.D., M.P.H., M.S.W., of the Kaiser Permanente Washington Health Research Institute in Seattle, is the corresponding author.
To access the embargoed study: Visit our For The Media website at this ...
#MedEd: How doctors use social media to advance medicine
2023-08-29
UNDER EMBARGO UNTIL 11:00 A.M. EDT ON TUESDAY, AUGUST 29, 2023
Social media’s effects on propagating misinformation among the lay public are widely debated, but a new paper from JAMA suggests physicians using social media are revolutionizing medical education.
La Jolla, Calif. (August 29, 2023) — Ever wonder what your doctor is doing on social media? A new study published in JAMA led by John W. Ayers, Ph.D., from the Qualcomm Institute within the University of California San Diego, finds some physicians are harnessing the reach ...
Underutilized antidepressant treatment for postnatal depression associated with improved child outcomes at age five
2023-08-29
New research led by the Institute of Psychiatry, Psychology & Neuroscience (IoPPN) at King’s College London has found that selective serotonin reuptake inhibitor (SSRI) treatment for postnatal depression is associated with improvements in child behaviour up to five years after childbirth.
Up to 15% of women experience postnatal depression which has been shown to be associated with poor outcomes for mothers’ and their children. Researchers at King’s IoPPN, in collaboration with the University of Oslo, analysed data from ...
Broken by bison, aspen saplings having a tough time in northern Yellowstone
2023-08-29
CORVALLIS, Ore. – In northern Yellowstone National Park, saplings of quaking aspen, an ecologically important tree in the American West, are being broken by a historically large bison herd, affecting the comeback of aspen from decades of over-browsing by elk.
Findings of the research led by Luke Painter of Oregon State University were published today in Ecology and Evolution.
The study comes five years after Painter, who teaches ecology and conservation in the OSU College of Agricultural Sciences, published a paper in Ecosphere showing that wolf reintroduction in Yellowstone had been a catalyst for aspen recovery both outside and ...
Partners from more than 100 countries collaborate as LOINC® issues 1,945 new concepts in semiannual release
2023-08-29
INDIANAPOLIS -- LOINC® from Regenstrief Institute is issuing its semiannual content update with 1,945 new concepts to help health systems, laboratories and other health organizations exchange medical data. The release contains newly created content based on requests submitted by stakeholders from more than 100 countries.
LOINC version 2.75 is available for download from the LOINC website and via the LOINC Terminology Service using HL7® FHIR®. The updated version includes new, edited and newly mapped concepts ...
New study will examine impact of lifestyle physical activity on cognition for older adults
2023-08-29
Jason Yang has been awarded nearly $400,000 from the National Institute on Aging to explore the role of lifestyle physical activity (light movements, walking) in cognition among insufficiently active older adults with higher risks for Alzheimer’s or related dementias. The exercise science assistant professor will use the two-year R21 grant to help determine if frequent and regular engagement in lifestyle physical activity over time may benefit cognitive function for this population.
A ...
More sleep could reduce impulsive behavior in children
2023-08-29
Sleep is a critical part of a child’s overall health, but it can also be an important factor in the way they behave.
According to a new study from the Youth Development Institute at University of Georgia, getting enough sleep can help children combat the effects of stressful environments.
“Stressful environments are shown to make adolescents seek immediate rewards rather than delayed rewards, but there are also adolescents who are in stressful environments who are not impulsive,” said lead author Linhao Zhang, a fourth-year doctoral student in UGA’s College of Family and Consumer Sciences. “We looked at what explains that link and what makes some people ...
LAST 30 PRESS RELEASES:
Exercise as an anti-ageing intervention to avoid detrimental impact of mental fatigue
UMass Amherst Nursing Professor Emerita honored as ‘Living Legend’
New guidelines aim to improve cystic fibrosis screening
Picky eaters by day, buffet by night: Butterfly, moth diets sync to plant aromas
Pennington Biomedical’s Dr. Leanne Redman honored with the E. V. McCollum Award from the American Society for Nutrition
CCNY physicists uncover electronic interactions mediated via spin waves
Researchers’ 3D-printing formula may transform future of foam
Nurture more important than nature for robotic hand
Drug-delivering aptamers target leukemia stem cells for one-two knockout punch
New study finds that over 95% of sponsored influencer posts on Twitter were not disclosed
New sea grant report helps great lakes fish farmers navigate aquaculture regulations
Strain “trick” improves perovskite solar cells’ efficiency
How GPS helps older drivers stay on the roads
Estrogen and progesterone stimulate the body to make opioids
Dancing with the cells – how acoustically levitating a diamond led to a breakthrough in biotech automation
Machine learning helps construct an evolutionary timeline of bacteria
Cellular regulator of mRNA vaccine revealed... offering new therapeutic options
Animal behavioral diversity at risk in the face of declining biodiversity
Finding their way: GPS ignites independence in older adult drivers
Antibiotic resistance among key bacterial species plateaus over time
‘Some insects are declining but what’s happening to the other 99%?’
Powerful new software platform could reshape biomedical research by making data analysis more accessible
Revealing capillaries and cells in living organs with ultrasound
American College of Physicians awards $260,000 in grants to address equity challenges in obesity care
Researchers from MARE ULisboa discover that the European catfish, an invasive species in Portugal, has a prolonged breeding season, enhancing its invasive potential
Rakesh K. Jain, PhD, FAACR, honored with the 2025 AACR Award for Lifetime Achievement in Cancer Research
Solar cells made of moon dust could power future space exploration
Deporting immigrants may further shrink the health care workforce
Border region emergency medical services in migrant emergency care
Resident physician intentions regarding unionization
[Press-News.org] Neural network helps design brand new proteinsA flexible, language-based approach proves surprisingly effective at solving intractable problems in materials science.