Faculty to use AI for Protein Design and Discovery with Support of $1.8 Million NIH Grant

The National Institute of Health (NIH) has awarded Yunan Luo a grant for more than $1.8 million to use artificial intelligence (AI) to advance protein research.

New AI models produced through the grant will lead to new methods for the design and discovery of functional proteins. This could yield novel drugs and vaccines, personalized treatments against diseases, and other advances in biomedicine.

“This project provides a new paradigm to analyze proteins’ sequence-structure-function relationships using machine learning approaches,” said Luo, an assistant professor in Georgia Tech’s School of Computational Science and Engineering (CSE).

“We will develop new, ready-to-use computational models for domain scientists, like biologists and chemists. They can use our machine learning tools to guide scientific discovery in their research.” 

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Luo’s proposal improves on datasets spearheaded by AlphaFold and other recent breakthroughs. His AI algorithms would integrate these datasets and craft new models for practical application.

One of Luo’s goals is to develop machine learning methods that learn statistical representations from the data. This reveals relationships between proteins’ sequence, structure, and function. Scientists then could characterize how sequence and structure determine the function of a protein.

Next, Luo wants to make accurate and interpretable predictions about protein functions. His plan is to create biology-informed deep learning frameworks. These frameworks could make predictions about a protein’s function from knowledge of its sequence and structure. It can also account for variables like mutations.

In the end, Luo would have the data and tools to assist in the discovery of functional proteins. He will use these to build a computational platform of AI models, algorithms, and frameworks that ‘invent’ proteins. The platform figures the sequence and structure necessary to achieve a designed proteins desired functions and characteristics.

“My students play a very important part in this research because they are the driving force behind various aspects of this project at the intersection of computational science and protein biology,” Luo said.

“I think this project provides a unique opportunity to train our students in CSE to learn the real-world challenges facing scientific and engineering problems, and how to integrate computational methods to solve those problems.”

The $1.8 million grant is funded through the Maximizing Investigators’ Research Award (MIRA). The National Institute of General Medical Sciences (NIGMS) manages the MIRA program. NIGMS is one of 27 institutes and centers under NIH.

MIRA is oriented toward launching the research endeavors of young career faculty. The grant provides researchers with more stability and flexibility through five years of funding. This enhances scientific productivity and improves the chances for important breakthroughs.

Luo becomes the second School of CSE faculty to receive the MIRA grant. NIH awarded the grant to Xiuwei Zhang in 2021. Zhang is the J.Z. Liang Early-Career Assistant Professor in the School of CSE.

[Related: Award-winning Computer Models Propel Research in Cellular Differentiation]

“After NIH, of course, I first thanked my students because they laid the groundwork for what we seek to achieve in our grant proposal,” said Luo.

“I would like to thank my colleague, Xiuwei Zhang, for her mentorship in preparing the proposal. I also thank our school chair, Haesun Park, for her help and support while starting my career.”