Researchers develop deep learning model that outperforms Google AI system in predicting peptide structures

Schematic diagram of the PepFlow architecture. Source: Nature Machine Intelligence (2024). DOI: 10.1038/s42256-024-00860-4

Researchers at the University of Toronto have developed a deep learning model called “PepFlow” that can predict any shape of a peptide, a chain of amino acids that is shorter than a protein but serves a similar biological function.

PepFlow combines machine learning and physics to model the range of folding patterns that peptides can adopt based on their energy landscape. Unlike proteins, peptides are highly dynamic molecules that can adopt many different conformations.

“Until now, it has not been possible to model all possible conformations of a peptide,” said Osama Abdin, lead author of the study, who recently completed his PhD in molecular genetics at the University of Toronto's Donnelly Centre for Cellular and Biomolecular Research. “PepFlow uses deep learning to capture precise, accurate conformations of peptides in just a few minutes. These models have the potential to aid in drug development through the design of peptides that act as binding agents.”

The research was published today in the journal Nature Machine Intelligence.

The role of peptides in the human body is directly related to how they fold, as their 3D structure determines how they bind and interact with other molecules. Peptides are known to be highly flexible and can adopt a variety of folding patterns, which allows them to participate in many biological processes that are of interest to researchers developing therapeutics.

“The focus of the PepFlow model was on peptides because they are incredibly important biomolecules and are highly dynamic in nature, so we need to model different conformations of peptides to understand their function,” said Philip M. Kim, lead researcher on the study and professor at the Donnelly Center. “Peptides are also important as therapeutic agents, as seen by GLP1 analogs such as Ozempic, which are used to treat diabetes and obesity.”

Kim, who is also a professor of computer science in the University of Toronto's Faculty of Arts and Sciences, said peptides are also cheaper to produce than larger proteins.

The new model extends the capabilities of AlphaFold, the leading Google Deepmind AI system for predicting protein structures. PepFlow outperforms AlphaFold2 by generating a range of conformations for a given peptide, which is not what AlphaFold2 was designed for.

What sets PepFlow apart is the technological innovation behind it: For example, PepFlow is a generalized model inspired by the Boltzmann Generator, an advanced physics-based machine learning model.

PepFlow can also model peptide structures that undergo unusual formations, such as ring-like structures that result from a process called macrocyclization. Peptide macrocyclization is currently a very promising area of ​​drug development.

Although PepFlow improves on AlphaFold2, it is the first version of the model and therefore has its own limitations. The study authors pointed out several ways in which PepFlow could be improved, such as training the model with explicit data on the solvent atoms that dissolve the peptide to form a solution, or constraints on the distances between atoms in ring-like structures.

PepFlow is built to be easily extended to account for additional considerations, new information, and potential applications. Even in its first version, PepFlow is a comprehensive and efficient model that may facilitate the development of therapeutics that activate or inhibit biological processes through peptide binding.

“Modeling with PepFlow gives us insight into the actual energy landscape of peptides,” says Abdin, “and although it took two and a half years to develop PepFlow and a month of training, it was worth it to move beyond models that predict only one peptide structure and into the next realm.”

Further information: Osama Abdin et al. “Direct conformational sampling from peptide energy landscapes by hypernetwork conditional diffusion.” Nature Machine Intelligence (2024). DOI: 10.1038/s42256-024-00860-4

Provided by University of Toronto

Citation: Researchers develop deep learning model that outperforms Google AI system to predict peptide structures (June 27, 2024) Retrieved June 27, 2024 from https://phys.org/news/2024-06-deep-outperforms-google-ai-peptide.html

This document is subject to copyright. It may not be reproduced without written permission, except for fair dealing for the purposes of personal study or research. The content is provided for informational purposes only.

Sources 1/ https://Google.com/ 2/ https://phys.org/news/2024-06-deep-outperforms-google-ai-peptide.html The mention sources can contact us to remove/changing this article

What Are The Main Benefits Of Comparing Car Insurance Quotes Online

LOS ANGELES, CA / ACCESSWIRE / June 24, 2020, / Compare-autoinsurance.Org has launched a new blog post that presents the main benefits of comparing multiple car insurance quotes. For more info and free online quotes, please visit https://compare-autoinsurance.Org/the-advantages-of-comparing-prices-with-car-insurance-quotes-online/ The modern society has numerous technological advantages. One important advantage is the speed at which information is sent and received. With the help of the internet, the shopping habits of many persons have drastically changed. The car insurance industry hasn't remained untouched by these changes. On the internet, drivers can compare insurance prices and find out which sellers have the best offers. View photos The advantages of comparing online car insurance quotes are the following: Online quotes can be obtained from anywhere and at any time. Unlike physical insurance agencies, websites don't have a specific schedule and they are available at any time. Drivers that have busy working schedules, can compare quotes from anywhere and at any time, even at midnight. Multiple choices. Almost all insurance providers, no matter if they are well-known brands or just local insurers, have an online presence. Online quotes will allow policyholders the chance to discover multiple insurance companies and check their prices. Drivers are no longer required to get quotes from just a few known insurance companies. Also, local and regional insurers can provide lower insurance rates for the same services. Accurate insurance estimates. Online quotes can only be accurate if the customers provide accurate and real info about their car models and driving history. Lying about past driving incidents can make the price estimates to be lower, but when dealing with an insurance company lying to them is useless. Usually, insurance companies will do research about a potential customer before granting him coverage. Online quotes can be sorted easily. Although drivers are recommended to not choose a policy just based on its price, drivers can easily sort quotes by insurance price. Using brokerage websites will allow drivers to get quotes from multiple insurers, thus making the comparison faster and easier. For additional info, money-saving tips, and free car insurance quotes, visit https://compare-autoinsurance.Org/ Compare-autoinsurance.Org is an online provider of life, home, health, and auto insurance quotes. This website is unique because it does not simply stick to one kind of insurance provider, but brings the clients the best deals from many different online insurance carriers. In this way, clients have access to offers from multiple carriers all in one place: this website. On this site, customers have access to quotes for insurance plans from various agencies, such as local or nationwide agencies, brand names insurance companies, etc. "Online quotes can easily help drivers obtain better car insurance deals. All they have to do is to complete an online form with accurate and real info, then compare prices", said Russell Rabichev, Marketing Director of Internet Marketing Company. CONTACT: Company Name: Internet Marketing CompanyPerson for contact Name: Gurgu CPhone Number: (818) 359-3898Email: [email protected]: https://compare-autoinsurance.Org/ SOURCE: Compare-autoinsurance.Org View source version on accesswire.Com:https://www.Accesswire.Com/595055/What-Are-The-Main-Benefits-Of-Comparing-Car-Insurance-Quotes-Online View photos