Lab exchange in Rosetta community

I am a postdoc in my final year in Prof. Bill DeGrado’s lab. During one of our weekly meetings, Bill and I discussed potential future research directions. He suggested that visiting another lab could broaden my perspective on protein design. After some thought, I realized that spending time in Prof. Jeff Gray’s lab would be an excellent opportunity.

I have been following Jeff’s research for years and have always been impressed by the innovative projects coming out of his lab, including developments related to PyRosetta, antibody design, protein docking, and especially glycan-protein binding studies. The last resonates strongly with my interest in designing proteins that recognize specific glycans.

I reached out to Jeff with a proposal to combine expertise from both labs to advance glycan-binding research. Jeff kindly accepted my application! Additionally, I was thrilled to receive support from the RosettaCommons lab exchange program, which helped cover part of the expenses for my visit.

I began my visit at the end of August, an ideal time to be in Baltimore. The warm weather complemented the beautiful Johns Hopkins University campus, with its lush green trees and iconic red-brick buildings.

My experience in Jeff’s lab exceeded all expectations. Jeff and Samuel Canner, an exceptionally talented graduate student in his lab, helped me brainstorm several potential research ideas. These included validating a glycan-binding protein database, segmenting glycan-protein binding motifs, and applying deep-learning diffusion models for glycan docking. This was my first in-depth exposure to using deep learning to predict biological molecules and building computational validation pipelines from scratch. Despite his busy schedule, Jeff took the time to discuss these projects with Sam and me weekly.

The supportive and collaborative lab environment was inspiring. Lab members generously shared their expertise, fostering productive discussions. I also appreciated the lab’s relaxed yet focused atmosphere and the weekly Friday group lunches generously provided by Jeff—thank you, Jeff!

One of the most valuable lessons I gained was learning to think computationally about protein design. In Bill’s lab, I primarily approached research by setting a design goal, applying computational strategies, and validating the designs through extensive experiments. Jeff’s lab taught me a computational mindset, emphasizing strategy and method development. Now that I am back in Bill’s lab as of November, I am collaborating with Sam on a project we hope to publish soon.

I am deeply grateful to Bill and Jeff for supporting this lab exchange. My thanks also go to Camille Mathis, Julia Koehler Leman, and others who facilitated the RosettaCommons program. Their efforts make RosettaCommons one of the most supportive scientific communities. The lab exchange program is an invaluable opportunity for graduate students and postdocs to gain new skills, build connections, and advance their careers.

– Lei Lu