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InnoCORE Research Group Successfully Achieves AI Protein Design with Nobel Laureate David Baker
< (From left) Professor Gyu Rie Lee, Professor David Baker >
Under the foundation of research cooperation established through the Ministry of Science and ICT's InnoCORE (InnoCORE) project, KAIST InnoCORE researchers have derived meaningful research results. Following a visit by Professor David Baker (University of Washington, USA), the 2024 Nobel Laureate in Chemistry, KAIST has revealed research findings on designing proteins that accurately recognize desired compounds using AI through joint research.
KAIST announced on April 9th that Professor Gyu Rie Lee of the Department of Biological Sciences—a researcher participating in the AI-CRED Innovative Drug InnoCORE Research Group—successfully designed artificial proteins that selectively recognize specific compounds using AI through joint research with Professor David Baker.
This research is characterized by using AI to design proteins that recognize specific compounds from scratch (de novo) and implementing them as functional biosensors. While the conventional approach mainly involved searching natural proteins or modifying some of their functions, this research is highly significant in that it ‘custom-built’ proteins with desired functions through AI-based design and even completed experimental verification.
In particular, the research team successfully designed a protein that selectively recognizes the stress hormone cortisol and implemented an AI-designed biosensor based on it. This is evaluated as a case that extends beyond protein design to actual measurable sensor technology, solving the long-standing challenge of small-molecule recognition in the field of protein design.
These research results are expected to be utilized in various fields such as disease diagnosis, new drug development, and environmental monitoring in the future. It can precisely detect biomarkers in the blood to diagnose diseases early and contribute to the development of targeted therapies through the design of proteins that selectively recognize specific molecules. Furthermore, it is expected that the implementation of customized biosensor technology will become possible, such as real-time monitoring of air and water quality through the development of sensors that detect environmental pollutants.
Designing new proteins (de novo proteins) that recognize compounds has been considered a challenge in the field of protein design for a long time because it requires precise calculations at the atomic level. The research team developed an AI model that precisely reflects protein-ligand interactions and successfully designed binding proteins using it.
As a result, artificial binding proteins were designed for six types of compounds, including metabolites and small-molecule drugs, and their functions were verified through experiments. In particular, a cortisol biosensor was developed by designing a chemical-induced dimer based on a new protein that binds with cortisol. A provisional patent for the relevant design technology has been filed in the United States.
Professor Gyu Rie Lee stated, “This research experimentally proves that AI can be used to design proteins that precisely recognize specific compounds,” and added, “We plan to expand this into protein design technology that can be utilized in various fields such as disease diagnosis, new drug development, and environmental monitoring in the future.”
Professor Gyu Rie Lee of the KAIST Department of Biological Sciences participated in this research as the first author, and Professor David Baker as the corresponding author. The study was published in the international academic journal Nature Communications on March 28, 2026. ※ Paper Title: Small-molecule binding and sensing with a designed protein family DOI: https://doi.org/10.1038/s41467-026-70953-8 Authors: Gyu Rie Lee, Samuel J. Pellock, Christoffer Norn, Doug Tischer, Justas Dauparas, Ivan Anishchenko, Jaron A. M. Mercer, Alex Kang, Asim K. Bera, Hannah Nguyen, Evans Brackenbrough, Banumathi Sankaran, Inna Goreshnik, Dionne Vafeados, Nicole Roullier, Hannah L. Han, Brian Coventry, Hugh K. Haddox, David R. Liu, Andy Hsien-Wei Yeh & David Baker
< Image of Research Content Summary >
Professor Gyu Rie Lee is a new professor who joined KAIST in February 2025 and leads the Protein Design Laboratory. She possesses world-class expertise in the field of precise protein complex design at the atomic level and is performing various research projects such as AI-based protein design, artificial enzyme design, and RNA-recognizing protein development. She is also participating as a mentor professor in the AI-CRED Innovative Drug Research Group of the InnoCORE project, conducting research on enzyme and peptide drug design.
Professor Lee conducted research as a postdoctoral researcher and Staff Scientist in Professor David Baker’s laboratory (University of Washington, USA, Howard Hughes Medical Institute) from 2018 to 2024. Professor David Baker is a world-renowned scholar in the field of protein structure prediction and design and was awarded the Nobel Prize in Chemistry in 2024.
Director Do-Heon Lee, a mentor professor of the AI-CRED Innovative Drug Research Group, stated, “This achievement is a meaningful result derived through cooperation between InnoCORE researchers and a global scholar,” and added, “We will further strengthen our research capabilities based on active research collaboration with postdoctoral researchers recruited through the InnoCORE project to continue creating innovative results in the AI drug development and bio-fields.”
Meanwhile, KAIST will host a lecture on Thursday, April 9th at 4 PM in the KI Building Fusion Hall featuring Professor David Baker and Professor Hannele Ruohola-Baker (University of Washington, USA) under the theme of ‘Advances in AI-powered protein design and biomedical science’ to mark Professor David Baker’s visit to Korea. This event is held with the support of the KAIST International Scholar Invitation Program, KAI-X, the InnoCORE AI-CRED Innovative Drug Group, and the Ministry of Science and ICT’s Overseas Excellent Research Institute Cooperation Hub Construction Project.
< Poster for Professor David Baker’s Invited Lecture >
KAIST President Kwang Hyung Lee stated, “Through cooperation with Nobel Laureate Professor David Baker, we have derived a meaningful achievement in AI-based protein design,” and added, “This research is an example showing that KAIST is leading innovative research alongside world-class research institutions.”
Meanwhile, the KAIST InnoCORE Research Group aims to accelerate AI-based scientific and technological innovation and promote global joint research by supporting top-tier domestic and international postdoctoral researchers to devote themselves to the development of AI convergence technology in a cutting-edge collective research environment. As the lead institution, KAIST operates the ▲Hyper-scale Large Language Model Innovation Research Group ▲AI-based Intelligent Design-Manufacturing Integration Research Group ▲AI-CRED Innovative Drug Research Group and ▲AI-Transformed Aerospace Research Group.
2026.04.09 View 2152 -
Professor Jae Kyoung Kim Receives the 2017 HSFP Award
The Human Frontier Science Program (HSFP), one of the most competitive research grants in life sciences, has funded researchers worldwide across and beyond the field since 1990. Each year, the program selects a handful of recipients who push the envelope of basic research in biology to bring breakthroughs from novel approaches. Among its 7,000 recipients thus far, 26 scientists have received the Nobel Prize. For that reason, HSFP grants are often referred to as “Nobel Prize Grants.”
Professor Jae Kyoung Kim of the Mathematical Sciences Department at KAIST and his international collaborators, Professor Robert Havekes from the University of Groningen, the Netherlands, Professor Sara Aton from the University of Michigan in Ann Arbor, the United States, and Professor Matias Zurbriggen from the University of Düsseldorf, Germany, won the Young Investigator Grants of the 2017 HSFP.
The 30 winning teams of the 2017 competition (in 9 Young Investigator Grants and 21 Program Grants) went through a rigorous year-long review process from a total of 1,073 applications submitted from more than 60 countries around the world. Each winning team will receive financial support averaging 110,000-125,000 USD per year for three years.
Although Professor Kim was trained as a mathematician, he has extended his research focus into biological sciences and attempted to solve some of the most difficult problems in biology by employing mathematical theories and applications including nonlinear dynamics, stochastic process, singular perturbation, and parameter estimation.
The project that won the Young Investigator Grants was a study on how a molecular circadian clock may affect sleep-regulated neurophysiology in mammals. Physiological and metabolic processes such as sleep, blood pressure, and hormone secretion exhibit circadian rhythms in mammals. Professor Kim used mathematical modeling and analysis to explain that the mammalian circadian clock is a hierarchical system, in which the master clock in the superchiasmatic nucleus, a tiny region in the brain that controls circadian rhythms, functions as a pacemaker and synchronizer of peripheral clocks to generate coherent systematic rhythms throughout the body.
Professor Kim said, “The mechanisms of our neuronal and hormonal activities regulating many of our bodily functions over a 24-hour cycle are not yet fully known. We go to sleep every night, but do not really know how it affects our brain functions. I hope my experience in mathematics, along with insights from biologists, can find meaningful answers to some of today’s puzzling problems in biological sciences, for example, revealing the complexities of our brains and showing how they work.”
“In the meantime, I hope collaborations between the fields of mathematics and biology, as yet a rare phenomenon in the Korean scientific community, will become more popular in the near future.”
Professor Kim received his doctoral degree in Applied and Interdisciplinary Mathematics in 2013 from the University of Michigan and joined KAIST in 2015. He has published numerous articles in reputable science journals such as Science, Molecular Cell, Proceedings of the National Academy of Sciences, and Nature Communications.
Both the Program Grants and Young Investigator Grants support international teams with members from at least two countries for innovative and creative research. This year, the Program Grants were awarded to research topics ranging from the evolution of counting and the role of extracellular vesicles in breast cancer bone metastasis to the examination of obesity from a mechanobiological point of view.
The Young Investigator Grants are limited to teams that established their independent research within the last five years and received their doctoral degrees within the last decade. Besides Professor Kim’s study, such topics as the use of infrasound for navigation by seabirds and protein formation in photochemistry and photophysics were awarded in 2017.
Full lists of the 2017 HFSP winners are available at: http://www.hfsp.org/awardees/newly-awarded.
About the Human Frontier Science Program (HFSP):
The HFSP is a research funding program implemented by the International Human Frontier Science Program (HFSPO) based in Strasbourg, France. It promotes intercontinental collaboration and training in cutting-edge, interdisciplinary research specializing in life sciences. Founded in 1989, the HFSPO consists of the European Union and 14 other countries including the G7 nations and South Korea.
2017.03.21 View 16398 -
Nobel Laureate Dr. John Michael Kosterlitz Speaks at KAIST
KAIST’s Department of Physics will invite one of three co-recipients of the Nobel Prize in Physics 2016, Professor John Michael Kosterlitz of Brown University, on January 9, 2017, to speak about the exotic states of matter, which is entitled “Topological Defects and Phase Transitions.”
Professor Kosterlitz shares the Nobel award with two other researchers, David Thouless and Duncan Haldane. He is considered one of the pioneers in the field of topological phases. In the early 1970s, along with Thouless, he demonstrated that superconductivity could occur at low temperatures and explained the mechanism behind, phase transition, that makes superconductivity disappear at higher temperatures.
Over the last decade, topological materials and their applications have been widely studied with the hope of using them in new generations of electronics and superconductors, or in future quantum computers. Details of the lecture follow below:
Distinguished Lecture Series by KAIST’s Physics Department
· Speaker: Professor John Michael Kosterlitz of the Physics Department,
Brown University
· Topic: “Topological Defects and Phase Transitions”
· Date: January 9, 2017, 4:00 PM
· Place: Lecture Hall (#1501), College of Natural Sciences (E6-2)
2017.01.06 View 11937 -
Visit by Sir Paul Maxime Nurse, President of the Royal Society
Sir Paul Maxime
Nurse, who is an English geneticist and cell biologist, visited KAIST and gave
a lecture entitled The Great Ideas of
Biology on March 11, 2014.
Sir Paul was awarded the 2001 Nobel Prize in
Physiology or Medicine with Leland H. Hartwell and R. Timothy Hunt for their discoveries
of protein molecules that control the division of cells in the cell cycle.
He was Professor of Microbiology at the University
of Oxford, CEO of the Imperial Cancer Research Fund and Cancer Research UK, and
President of Rockefeller University in New York. Sir Paul is currently the President of
the Royal Society as well as Director and Chief Executive of the Francis Crick
Institute.
Founded in London in 1660, the Royal Society is composed of the world’s most distinguished scientists drawn from all areas of
science, engineering, and medicine.
Below is a summary of his lecture, The Great Ideas of Biology:
Four major ideas of biology
are the theory of genes, evolution by natural selection, the proposal that the
cell is the fundamental unit of all life, and the chemical composition of a cell.
When considering the
question “what is life?” these ideas come together. The special way cells reproduce
provides the conditions by which natural selection takes place, allowing living
organisms to evolve. The organization of chemistry within the cell provides
explanations for life’s phenomena.
In addition, an emerging idea
is the nature of biological self-organization with which living cells and organisms
process information and acquire specific forms. These great ideas have
influenced one another and changed the way we perceive biology and science
today.
2014.03.11 View 16277 -
U.S. Nobel Laureate to Run Korea's Top Tech University
Robert Laughlin,
President of the Korea Advanced Institute of Science and Technology (KAIST)
DAEJEON, July 14 (Yonhap) -- Nobel Physics Prize laureate Robert Laughlin was sworn in Wednesday as the first foreign president of the Korea Advanced Institute of Science and Technology (KAIST), South Korea"s top technology university.
Laughlin, in his inauguration speech, pledged to transform the state-run Korean university into a globally competitive educational institution, while also vowing to make it research oriented.
"Many people have asked me how I, as a foreigner, could possibly understand the situation here at KAIST, much less figure out a path forward," he said. "The short answer is that the situation here is not unique. The problems facing the research university are historical in nature and essentially identical all over the world."
He added the same worried discussions are taking place in other universities around the globe such as at Stanford, the Massachusetts Institute of Technology, Heidelberg and Tokyo.
"I have come here not to solve your problems but to solve my own," the 54-year-old American said.
Laughlin said KAIST is a large, well-functioning organization for which few things needed to be changed.
The former Stanford University professor also promised to work hard to lead the university in a novel direction.
"All of us in the technical university have a holy obligation ... we are here for the sole purpose of having big dreams and finding the strength to make them come to pass," Laughlin said.
"As far as I"m concerned, my job comes down to one thing: to make sure that your dreams are big enough, and to help everyone here -- faculty and students -- find the means to make them come to pass. That"s all," he said.
The ceremony was attended by Science and Technology Minister Oh Myung, Daejeon City Mayor Yeom Hong-chul and U.S. Ambassador to South Korea Thomas Hubbard, among others.
On Thursday, Laughlin is scheduled to meet President Roh Moo-hyun in Seoul. Laughlin will start his four-year term from mid-August, KAIST said.
Laughlin won the Nobel Prize for Physics in 1998 with Horst Stoermer of Germany and Daniel Tsui of the United States for discovering a new form of quantum fluid that gives more profound insights into the general inner structure and dynamics of matter.
On May 28, he was chosen to run the Korean university at a board meeting. (END)
2004.07.15 View 21202 -
Nobel Laureate Heads KAIST
Nobel Laureate Heads KAIST
By Kim Tae-gyu / Staff Reporter
THE KOREA TIMES 05-29-2004
A Nobel laureate will lead the Korea Advanced Institute of Science and Technology (KAIST), winning a stiff race with a pair of strong Korean candidates.
The KAIST on Friday said the state-financed institute appointed Robert Laughlin as its 12th president instead of two local hopefuls, professors Shin Seong-cheol and Park Seong-ju.
This is the first time that foreigners take charge of the KAIST since it was established in 1971 and Laughlin also is noted in the history as the first Nobel Prize winner to head Korea"s educational institute.
After receiving approval of Science-Technology Minister Oh Myung, Laughlin will be inaugurated as early as next month, according to a KAIST official.
Laughlin, a Stanford professor, made his name after being co-awarded the 1998 Nobel Prize in Physics with Horst Stoermer and Daniel Tsui for the discovery of a new form of quantum fluid.
The findings, which explained the fractional quantum hall effect for the first time, have been recognized as a significant breakthrough in understanding quantum physics.
The American physicist had also sustained a special connection with Korea even before he garnered the prestigious prize and has visited Korea several times.
Early last month, Laughlin was named to head the Asia Pacific Center for Theoretical Physics (APCTP) in recognition of his notable interest in Korea.
The APCTP is an international research institute headquartered inside Pohang University of Science and Technology in North Kyongsang Province.
voc200@koreatimes.co.kr
2004.05.31 View 27120