Saving real lives with artificial intelligence

Better treatments for cancer, autoimmune diseases, viruses and more are on the horizon thanks to AI-powered work from the UW scientists at the Institute for Protein Design.

Some of the Institute for Protein Design’s “communal brain,” including UW students, faculty and staff. Left to right: Christina Savvides, Gizem Gökçe-Alpkılıç, Ria Sonigra, Yulia Politanska, Prof. David Baker, Samir Faruq, Andrew Borst, Roman Barth, Meg Lunn-Halbert, Daniel Pfalmer

Biochemistry undergrad Samir Faruq gets experience with lab research and applying concepts from the classroom.��

Excitement is in the air for Samir Faruq, ’26, each week as he enters the light-filled fourth floor of the Nanoengineering & Sciences Building on the �� campus. Beyond the hands-on research skills he’s learning, there’s the buzz of possibility — the chance to contribute to a lifesaving new medicine just around the corner. “It’s so cool,” Faruq says, “knowing that the work I’m doing contributed to the Nobel Prize.”

This is the home of the UW’s (IPD), founded and led by Professor David Baker, a winner of the 2024 Nobel Prize in Chemistry. This cross-disciplinary institute is harnessing artificial intelligence to shape the future of medicine and beyond, work that will improve people’s lives. At the heart of that work are the faculty members, doctoral students, postdoctoral researchers, staff members and undergraduates like Faruq, who come from all parts of the country and the world.

“We look at some of the biggest problems that confront humanity. And then we think, ‘Could we design proteins to address those problems?’”

David BakerDirector, UW Institute for Protein Design; 2024 Nobel Prize in Chemistry

Baker describes the IPD as a “communal brain”— a network of connected people from different fields of study, each contributing their unique perspectives, ideas and expertise to solve complex challenges in medicine, technology and sustainability. “We look at some of the biggest problems that confront humanity,” says Baker, a Seattle native who has spent a lifetime studying proteins and founded the IPD at UW Medicine in 2012. “And then we think, ‘Could we design proteins to address those problems?’”

Hear from IPD students, faculty and staff about how they're using AI to create real solutions that can change lives.

The power of proteins

Proteins are the basic building blocks of all life. Baker and his fellow biochemists have been studying these versatile tiny machines for decades, knowing they could be the key to everything from defeating diseases to cleaning up environmental toxins. But UW scientists at the IPD have sped up this research by harnessing AI, and they are now creating new proteins from scratch. In short, they’re doing what nature has evolved to do over billions of years — with a few clicks of a computer.

The impact of this new frontier of science is broad, but it’s especially life-changing in medicine, where it has the potential to unlock new treatments for Alzheimer’s disease, cancer, autoimmune disorders and more. That’s because proteins play many important roles in the human body: transporting oxygen throughout your bloodstream, digesting food, powering your muscles and defending against infections.

While AI has been vital in accelerating this work, it’s the collective power of the Huskies at the institute that drives it forward, with funding from federal research grants, industry partners and philanthropy. It’s work that can make a difference in people’s day-to-day lives and lifetimes. And each person in this communal brain has a role to play — starting with Professor Baker.

The IPD attracts students and researchers from all over the country and the world.

A 3D-printed model of a synthetic protein designed to break down gluten, which is being clinically tested to treat celiac disease.

A trailblazer in protein design

Protein design is a new field of biology, one that Baker helped found. Scientists have been trying to construct synthetic proteins since the late 1980s — and while Baker’s team made many breakthroughs, one piece of the challenge eluded them: quickly predicting the protein’s unique shape. The way a protein coils itself up into a specific shape determines what it can or can’t do. It’s the key to creating proteins that carry out specific tasks, like binding to cancer cells so they can be found and treated.

David Baker speaking with 2 scientists in lab — *Baker, shown here in his lab, was awarded the 2024 Nobel Prize in Chemistry for his groundbreaking work in computational protein design.*

About seven years ago, IPD researchers started experimenting with artificial intelligence. Using a deep-learning tool — an AI approach that analyzes patterns in data to make predictions — they trained it to predict how proteins would fold.

UW students help test AI-designed proteins in the lab.

Suddenly, complex work that might have taken years in the lab could be done in minutes on a computer. This discovery was named the 2021 Breakthrough of the Year by the American Association for the Advancement of Science and helped lay the groundwork for Baker’s 2024 Nobel Prize.

Today, the team’s suite of homegrown AI tools for modeling and generating proteins are even more sophisticated. “It’s fun to see how fast things are moving,” says Baker about the progress he’s seen over the past few years. “We release our AI methods for anyone to use, so we’re seeing an acceleration of protein design across the world.” More people working in protein design means more new medicines in the future.

Designing hope for patients

Grad student Christina Savvides, who’s working toward doctorates in medicine and molecular engineering, is researching a better treatment for rheumatoid arthritis, a chronic autoimmune disorder.

That possibility is what brought Christina Savvides, who’s working toward a UW medical degree and a doctorate in molecular engineering, to the IPD.

“I want to be what is called a physician scientist,” says Savvides, who chose the UW for its top-notch medical training program and collaborative research environment. “A core principle is the idea of ‘bench to bedside,’” she explains, referring to a medicine’s journey from being developed in the lab to becoming available to patients. “I want to offer something to patients who have no viable treatment options.” The protein research she’s currently working on could be that hope.

Because the human body runs off of proteins, they’re the key to unlocking new ways to prevent and treat diseases, including cancer. “One of the challenges in recognizing cancer cells has been they don’t look very different from normal cells,” Baker says. “We’ve recently developed a technology that can measure key markers of cancer proteins. This gives us a whole new way of targeting cancer cells.”

Other IPD breakthroughs that might save or improve lives could include an effective antivenom for snakebites, a universal flu shot you’d need only once in your life, antibiotics designed to combat drug-resistant bacteria, a better vaccine to prevent malaria (the number-one killer of young children worldwide) and treatments for autoimmune disorders like rheumatoid arthritis.

Savvides describes the current treatment options for rheumatoid arthritis as a “sledgehammer” approach. While these medications work well, they result in collateral damage to tissue and organs, and many people opt to stop treatment. Her goal is to find the key to target just the immune system “and avoid that destruction.”

“I want to offer something to patients who have no viable treatment options.”

Christina SavvidesM.D./Ph.D. Candidate, Molecular Engineering

The process of getting a new medical treatment from a university lab to patients is complex, requiring clinical trials and approvals from regulators. The IPD has a robust pipeline to kick things off by that can, for example, test and commercialize new medicines so they can get to doctors and patients. So far, Baker has launched 21 biotech companies, many of them in Seattle — with more on the horizon. That includes , the single largest new biotech firm in 2024, with $1 billion in committed funding.

The UW is the ideal place for new medical discoveries to take off, Baker says, because of its collaborative culture and location. He adds: “Seattle is a great place for this work because of the resources and expertise in the city.”

Accelerated by AI

These exciting new developments rely on fast, accurate AI tools — and the expertise of research scientists like Andrew Borst, ’19, with a giant microscope that takes up half of a basement room.

two scientists looking at computer screen — *Staff scientists Andrew Borst and Daniel Pfalmer use a high-powered electron microscope to test AI-designed proteins in real life.*

Borst leads a team that uses a high-powered electron microscope to see if the lab proteins match their computer-generated blueprints. He often thinks back to a pivotal moment in December 2022: the first time every AI-designed protein that came under his microscope was behaving in real life exactly as the computer models had predicted. It meant the institute’s AI tools weren’t just fast — they were also accurate. And that opened exciting possibilities, especially for new medicines.

Part of what sets the IPD apart is this combination of computational and lab work, where promising AI-designed proteins are produced in the lab and then tested. On one side of the IPD, researchers huddle around computers to talk through programming code and examine vibrant models of possible proteins — cylindrical, circular and ribbonlike shapes that dance on screens. And nearby through gleaming glass doors, white-coated team members navigate around each other in a lab as they set up experiments to validate and modify the AI designs.

A 3D-printed model of a protein designed to target a vulnerable part of the 1918 influenza virus.

In this model, the small proteins in blue and white, forming spheres just 30 nanometers tall, can become protective vaccines when combined with fragments of a virus.

Testing is often an iterative process, requiring the designer to go back to the drawing board or tinker with the algorithm to get the protein’s shape and function right. It’s equal parts exciting and frustrating. And it’s what brought Borst to the UW.

“I chose the UW for graduate school because I wanted to be where groundbreaking research was performed,” says Borst, who grew up in Everett, earned his UW doctoral degree in biochemistry and is now IPD’s head of electron microscopy. Over his 15 years at the UW, he’s watched how AI has magnified the impact of that research.

Communal brain, community impact

This work is already rapidly reshaping medicine — and improving people’s lives. The IPD helped develop now used in the United Kingdom and South Korea; it was the world’s first medicine based on a computer-generated protein. Multiyear flu vaccines from the IPD are also in clinical testing, and recent IPD breakthroughs could lead to new, more effective cancer treatments.

None of these discoveries would be possible without the IPD’s communal brain — from undergraduates like Faruq and grad students like Savvides to staff researchers like Borst — building on decades of past research from Baker and fellow scientists.

The impact of this new frontier of science is broad, but it’s especially life-changing in medicine, where it has the potential to unlock new treatments for Alzheimer’s disease, cancer, autoimmune disorders and more.

Four people sitting around table with laptops — *Students at the IPD learn to collaborate and communicate about their research in clear, easy-to-understand ways — skills for any future career.*

“When smart, motivated, passionate people are interacting all the time, the greater the science — and the harder the problems that can be solved,” says Baker, who’s never far from the lab and makes himself readily available to students. His goal is for his trainees to walk away with both a love for research and the skills in creative problem-solving and collaboration that will serve them in any career path.

That’s been the case for Faruq, who’s been involved with the IPD since 2023; he’s given presentations on his work and learned hands-on skills from a graduate student mentor. A plus is knowing his undergraduate research has real-world impacts. “My mentor was talking about finding ways to combat antibiotic resistance — that’s what drew me in,” says Faruq, who hopes to attend medical school after graduation.

When Baker went to Stockholm to accept the Nobel Prize in Chemistry, a quarter of the audience were people he’d worked with — former members of the communal brain who had gone on to become professors or run companies. “Making scientific discoveries is one thing,” he says, “but training and mentoring people who go on to do wonderful things is my real role.”

Meet members of the Baker Lab’s “Communal Brain”

Andrew Borst, ’19

Andrew Borst, ’19

Everett, Washington
Research scientist

Research focus: Ensuring AI-generated proteins work in the real world

“We’re seeing Seattle become a new type of Silicon Valley, using computational protein design to help solve a lot of problems in medicine that currently don’t have any solutions.”
Christina Savvides, ’29

Christina Savvides, ’29

Shaker Heights, Ohio
Medical and Doctoral Candidate, Molecular Engineering and Sciences

Research focus: New therapies for rheumatoid arthritis

“By using AI, we can create therapies that better target disease while minimizing risks for patients, ultimately making treatments safer and more personalized.”
Daniel Pfalmer

Daniel Pfalmer

North Pole, Alaska
Research Scientist

Research focus: A more effective vaccine for malaria

“Eighty percent of deaths from malaria are in children under 5. The sooner I get this work done, the sooner we can have a vaccine that could be saving the lives of children.”
Gizem Gökçe-Alpkılıç, ’26

Gizem Gökçe-Alpkılıç, ’26

Ankara, Turkey
Doctoral Candidate,��Molecular Engineering and Sciences

Research focus: Targeted disease treatments using custom peptides (mini-proteins)

“Ever since I was a kid, I dreamed of finding ways to make people healthier through science. But the idea of engineering molecules to fight diseases? That’s what truly excites me.”
Meg Lunn-Halbert, ’27

Meg Lunn-Halbert, ’27

Olathe, Kansas
Doctoral Candidate, Biochemistry

Research focus: More effective vaccines that work with your body

“Vaccine adjuvants help your body have a better immune response. It means you can be better protected against disease and need less of the vaccine — a win-win!”
Ria Sonigra, ’28

Ria Sonigra, ’28

Pune, India
Doctoral Pre-Candidate, Molecular Engineering and Sciences

Research focus: Better diagnostic tools for medicine and beyond

“What I’m working on will make diagnostics 10 times faster and easier to do from home! The same technology could also detect how much fertilizer or pesticide is present in food.”
Roman Barth

Roman Barth

Forst, Germany
Postdoctoral Researcher

Research focus: Building new molecular machines using nature’s example

“Proteins are minuscule machines doing all the work in our body. Like engines in our cars, they run on fuel and convert the energy into mechanical work.”
Samir Faruq, ’26

Samir Faruq, ’26

St. Louis, Missouri
Undergraduate, B.S. in Biochemistry, Minor in Human Rights

Research focus: Targeted antibiotics for catheter-associated urinary tract infections

“I’ve been able to apply the concepts I’ve learned in classes. One time, I learned something in my biochemistry class about protein purification and later did protein purification in the lab.”
Yuliya Politanska, ’27

Yuliya Politanska, ’27

Chernivtsi, Ukraine
Doctoral Candidate, Biochemistry

Research focus: Designing specialized proteins that turn genes on and off

“When I started grad school, I didn’t know how to code and had to pick up those skills on the fly. But the Baker Lab was a great place to do that because there’s so many different people with different expertise.”
David Baker

David Baker

Seattle, WA
Professor of Biochemistry
Director, Institute for Protein Design
2024 Nobel Prize in Chemistry

“Protein design is this incredibly powerful new approach to solve all these pressing problems facing humanity. People know that the UW is the place to come do that.”