As a young child, Gizem Gökçe-Alpkılıç asked her parents for a microscope to allow her to dissect the world around her. She’s still looking at life’s smallest parts today at the UW’s Institute for Protein Design (IPD) — just with a few more sophisticated tools at her disposal.
Led by Nobel Prize winner David Baker, the IPD is an interdisciplinary research center that’s harnessing artificial intelligence to design new proteins — the building blocks of biology — to shape the future of medicine and beyond. The real-world impact of this cutting-edge research is what brought Gökçe-Alpkılıç, ’26, halfway across the world from her hometown in Ankara, Turkey, to the UW for a doctorate in molecular engineering.
And it’s what’s keeping her at the IPD as a postdoctoral researcher, after graduating this spring. Gökçe-Alpkılıç’s work could help scientists solve persistent global challenges, like infections from bacteria or viruses that have adapted to the medicines that typically kill them. “We need new countermeasures and we need to be fast,” she says, “so AI models will be helpful in that part.”
Gökçe-Alpkılıç’s Husky journey began long before she arrived on campus in Seattle as a doctoral student. In 2015, as an undergraduate in Turkey studying biomedical engineering, she spent four meaningful months at the UW through the Visiting International Student Internship & Training (VISIT) program. Working in Chemical Engineering Professor François Baneyx’s lab gave her a firsthand experience with research — and a sense for her future as a scientist, one that she’d been dreaming about since she asked for that microscope.
She was hooked, both on research and on the UW. She even snapped a photo of herself hugging the bronze W statue on campus, with a promise to be back. A few years later, with support from a scholarship from the Turkish Fulbright Education Commission, she fulfilled that promise to herself. What initially drew her to the University — the resources, community and interdisciplinary collaboration — brought her to the UW’s Institute for Protein Design.
What she couldn’t have predicted when she began her doctoral studies is how AI tools would rapidly accelerate and transform the field, allowing scientists to quickly test hundreds of potential protein designs and create new proteins that don’t exist in nature.
Part of what sets the IPD apart is how Gökçe-Alpkılıç and her colleagues combine time in front of the computer — using deep-learning tools to model and generate protein designs — with time wearing white coats and goggles, testing their designs in a laboratory. “It’s really important to use experimental data and feed it back to the AI computational models to improve it further,” she says.
Computational AI-powered tools allow scientists like Gökçe-Alpkılıç to quickly design hundreds of proteins.
Testing those designs in the lab provides experimental data to improve the AI-generated models.
Harnessing these homegrown AI tools in the Bhardwaj Lab, Gökçe-Alpkılıç has tested the capabilities of peptides, tiny molecules that can target specific proteins associated with diseases like cancer or antibiotic-resistant bacteria. Think of proteins as a lock and peptides as the key, she says: “You basically know the structure of your lock and are trying to make the key to fit into that.” Her goal is to find the key that both fits and stays in the lock. These new peptides can pave the way for highly targeted drugs for infections and diseases that don’t currently have effective treatments or prevention measures.
After successfully defending her dissertation and graduating in spring 2026, Gökçe-Alpkılıç is continuing her work as a postdoctoral researcher in the UW Institute for Protein Design.
A lot of her research has focused on a particular protein in Francisella tularensis, a bacterium that causes a rare disease called tularemia. There’s no licensed tularemia vaccine available in the U.S., and the bacterium is classified as a potential bioterrorism agent. She has been working to design peptide or mini-protein binders that could interfere with the protein’s function, but there is still more learning and work to be done.
The UW is the right place for this kind of exploratory research. “If you have an idea, you develop a hypothesis,” she says, “and because you have great computational resources, you can set up experiments in a few days to test it out.”
And she’s excited to see where her research could go next — far beyond anything she’d imagined as a child with a brand-new microscope.
Hear from Gökçe-Alpkılıç about how scientists like her harness AI to develop new solutions to rising challenges.
Story by Malavika Jagannathan // Photos by Mark Stone and provided by Gizem Gökçe-Alpkılıç
Originally published June 2026
