IPD Open House

( 4.23.26  )                                    Written by Gio Kim                          

I first cold emailed the Baker Lab in order to pursue my passion to get closer to the kind of work that actually interests me, which is the intersection of computational systems biology and protein. I was not expecting much. The email was a shot in the dark, a way to test whether there was any path into the kind of research environment I had been reading about. What came back was technically a rejection, but it was not the end of the conversation. Instead, I was invited to the Institute for Protein Design Open House on April 17th, and that invitation gave me a direct look into a field that felt much closer to the kind of future I want to build for myself.

The open house took place at UW’s Molecular Engineering and Sciences building, and stepping into the conference room gave a whole new sense of environment: seeing the world renowned faculty members made it clear that this was not some surface level event. The talks moved quickly through protein design, immunomodulation, tau binder design, antigen display, mRNA vaccines, enzyme design, and conformational dynamics. Even though each speaker focused on something different, the bigger theme was clear; none of this work treated proteins as fixed objects, rather, they were presented as dynamic systems with structure, behavior, and function that can be deliberately changed. That idea is what makes this field so compelling to me.

The talk that stayed with me most was Kathryn Shelley’s presentation on conformational dynamics. The idea that a protein can be engineered to shift shapes and even return to its original form using light felt especially powerful. It was not just about understanding structure. It was about controlling structure in a way that changes function. That is the kind of thinking that pulls me toward computational systems biology. I do not just want to look at biological parts in isolation. I want to understand how components interact, how those interactions produce behavior, and how computation can be used to predict and shape those outcomes.

I also found the antigen display work especially interesting because it made the design side of biology feel almost architectural. The use of octahedral nanoparticles to present multiple mRNA strands showed how precise the field can be when structure is used strategically. It was a reminder that biology is not only about chemistry or sequence. It is also about organization, geometry, and system-level control.

The lab tour made all of that feel even more real. Seeing both the wet and dry lab spaces showed me that this field depends on a tight connection between computation and experiment. The work is not just theoretical modeling or just bench science. It is a pipeline where design, testing, and iteration all feed into each other. Seeing their tradition of 3D printing proteins and walking past a newspaper celebrating David Baker’s Nobel Prize recognition made the environment feel both technically advanced and deeply alive.

I left with a stronger understanding of tools like RFdiffusion, PyRosetta, and PyMOL, but more importantly, I left with a clearer sense of direction. This experience showed me that computational systems biology is not just an interest I have in theory. It is the kind of work I want to keep moving toward in practice.

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