Seattle, Washington, United States
I integrate biophysical data into protein structure prediction networks to improve protein modeling and protein design. I've worked primarily with cryo-EM density, but I'm also interested in NMR chemical shifts and other data relevant to enzyme activity. I'm fascinated by enzymes and read about their reaction mechanisms in my spare time. I've worked on a handful of deep learning-based protein folding networks, such as RoseTTAFold2-allatom, (cycling between the coordinate update and a novel density update) then AlphaFold3 (using guided diffusion) and briefly Boltz-1. In graduate school I integrated electron density into protein structure prediction for automated structure refinement. I rotated in the Stoll lab, extending the backbone-dependent rotamer library to the EPR spin label, R1 using Monte Carlo molecular dynamics. In undergrad I studied the history and coverage of biomolecular representations in computer memory, and dabbled in genetic code expansion. My work has also applied these protein modeling methods for protein design, using ProteinMPNN, Protein Inpainting, and AlphaFold2 to design novel heme peroxidases. Parallel to my research career, I've built a strong instructional skillset at multiple levels of higher education. I TA'd mathematics and junior-level Physical Chemistry in undergrad and junior-level Biochemistry in graduate school. Under Dr. Liangcai Gu, I prepared and delivered a lecture on the genetic code translation machinery to 50 undergraduates. I then co-created the Biochemistry Undergraduate Reading Program with fellow grad student Annabel Vernon, where over 200 undergraduates have since explored the literature with a graduate or postdoctoral mentor.
Rotation labs: - Stefan Stoll - David Baker - Frank DiMaio
I scanned over 700 peer-reviewed articles to determine how scientists have represented biomolecules in computer memory. I built a taxonomy from the over 1000 distinct features I found, and published an article summarizing my findings
Undergraduate Research Assistant at Oregon State University, in Ryan Mehl's Lab, under Dr. Subhashis Jana, Riley Bednar and Nathan Waugh. Primarily leveraging Genetic Code Expansion technology to site-specifically incorporate unnatural amino acids into target proteins to study the following: Project List: - Expanded genetic code of new tetrazine amino acids with aaRS/tRNA pair screening and design - Enzyme Surface Immobilization - Enzyme Orientation on Activity - Heteroprotein Complexes