Better treatments for cancer and beyond are on the horizon thanks to the philanthropy-powered, AI-enabled work of the UW Institute for Protein Design.
There's a buzz of possibility in the air. On one side of the Nanoengineering & Sciences Building's light-filled fourth floor, researchers huddle around computers to talk through the latest machine-learning architectures and examine cylindrical, circular and ribbonlike shapes that dance on screens—models of possible proteins. And on the other side, through the gleaming glass doors of a lab, white-coated team members set up experiments to manufacture and test those AI-generated molecules.
This is the home of the University of Washington’s Institute for Protein Design (IPD), founded and led by Professor David Baker, a winner of the 2024 Nobel Prize in Chemistry. This cross-disciplinary research center on campus is harnessing artificial intelligence to shape the future of medicine, technology, the environment and beyond—work that’s already improving people’s lives. And it’s all possible thanks to a combination of private support, federal funding and industry partnerships.
“We look at some of the biggest problems that confront humanity,” says Baker, a trailblazer in protein design who founded the IPD at UW Medicine in 2012. “And then we think, ‘Could we design proteins to address those problems?’”
Proteins are the basic building blocks of all life. Baker and his fellow biochemists have been studying these versatile tiny machines for decades, excited by their potential to do 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’re 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.
Philanthropic gifts played a key role in pushing this research forward, especially when the work with AI was largely theoretical and not widely understood enough to attract federal funding.
David Baker
“There were cases where the federal funding system would have thought it was too far out—and philanthropy really helped us,” says Baker, who was instrumental in establishing protein design as a promising new field of biology. “We’ve been incredibly fortunate to work with visionary philanthropists who supported our work when what I described seemed like science fiction.”
Those visionary investments helped turn science fiction into science reality.One example is a five-year gift from philanthropic funder and adviser Open Philanthropy, which allowed Baker and colleagues to reimagine their protein-folding software using deep learning—an AI approach that analyzes patterns in data to make predictions. The new tools they built have radically sped up advances in the field, helping lay the groundwork for Baker’s Nobel Prize and creating a new frontier of science.
The impact is especially life-changing in medicine, where new proteins have the potential to treat 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.
“It would be an absolute disaster for us and for American science if students cannot continue their education because of funding cuts.”
Professor David Baker
That enormous potential is what attracted Christina Savvides, ’29, to the IPD. She’s working toward a UW medical degree and a doctorate in molecular engineering, thanks in part to the Oren Traub Endowed Fellowship, which supports students enrolled in the UW School of Medicine’s Medical Scientist Training Program.
“I want to be what is called a physician scientist,”says Savvides, who chose the UW for its top-notch 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 now working on could be that hope for people with rheumatoid arthritis.
Savvides describes the current treatment options for this painful autoimmune disorder as a “sledgehammer” approach. These medications are not elective for all patients—and for those who do respond, the medicines can cause collateral damage to tissue and organs. Though patients may continue treatment despite the side effects, many are unhappy with their current options. Savvides’ goal is to find the key to target just the immune system “and avoid that destruction.”
The IPD has already successfully created one medicine based on computer-generated proteins: a COVID-19 vaccine authorized in the United Kingdom and South Korea. Other IPD breakthroughs that might save or improve lives include new antivenoms for snakebites, a flu shot you may need only once in your lifetime (currently in clinical testing), antibiotics that combat drug-resistant bacteria, a better vaccine to prevent malaria—the number-one killer of young children worldwide—and more effective cancer treatments.
“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.”
Getting a new medical treatment from a university lab to patients is a complex process, requiring clinical trials and approvals from regulators. Spinout companies play a role by testing and commercializing new medicines so they can get to doctors and the patients who’ll benefit from them. So far, Baker has launched 21 biotech companies, many of them in Seattle—including the single largest new biotech firm in 2024.
And philanthropy remains a crucial piece of the process. “This is a time when people can support absolutely critical research,” Baker says. He notes that, like the visionary philanthropy that opened doors for the IPD’s beginnings, today’s support can push on-the-cusp discoveries forward and transform people’s health and well-being everywhere.
A 3D-printed model of a protein designed using AI-powered tools.
There are UW graduate students like Savvides behind every breakthrough at the Institute for Protein Design—from innovative AI tools to cancer-targeting proteins.
“They drive innovation and discovery in our research group,”says Baker about the IPD’s 92 current doctoral students, who are training to become the future doctors, faculty, researchers and biotech company leaders of America.
For decades, state and federal funding has created a vital pathway for graduate students—but recent cuts are forcing many to walk away from their education and critical research. “It would be an absolute disaster for us and for American science,” Baker notes, “if students cannot continue their education because of funding cuts.”
That’s why the UW is launching a bold, University wide initiative for graduate student support. When you support the Graduate Student Research Resilience Fund, you can make an immediate impact for students like Savvides and the lifesaving work she’s doing at the UW—and keep the discoveries coming.
Learn more about supporting the Graduate Student Research Resilience Fund.