Speaker: Ellen Zhong, Assistant Professor, Princeton University, Computer Science 

Title: Machine Learning for Structural Biology

Day: April 16, 2024 

Place: CSML,  Bendheim House, 26 Prospect Ave, Classroom Room 103

Time: 12:30-1:30 PM Lunch available from 12:00    

Host: Tom Griffiths, Director CSML

Abstract: Structural biology has been transformed by breakthroughs in deep learning methods for protein structure prediction. In parallel, advances in cryo-electron microscopy (cryo-EM) have produced new opportunities to study the structure and dynamics of proteins and other biomolecular complexes through imaging. In this seminar, I will overview cryoDRGN and related methods that leverage the representation power of deep neural networks for 3D reconstruction of protein structures from cryo-EM images. Extended to real datasets and released as open-source tools, these methods have been used to discover new protein structures and visualize continuous trajectories of protein motion. I will discuss extensions of the method for scalable and robust reconstruction, analysis of the learned generative model, and visualization of dynamic macromolecular machines in situ. Finally, I will discuss how recent advances in machine learning for protein structure prediction (e.g. AlphaFold) can complement methods for cryo-EM structure determination and what key algorithmic challenges remain to realize the next era of structural biology.

Bio: Ellen Zhong is an Assistant Professor of Computer Science at Princeton University. She is interested in problems at the intersection of AI and biology. Her research develops machine learning methods for computational and structural biology problems with a focus on protein structure determination with cryo-electron microscopy (cryo-EM). She obtained her Ph.D. from MIT in 2022, advised by Bonnie Berger and Joey Davis, where she developed deep learning algorithms for 3D reconstruction of dynamic protein structures from cryo-EM images. She has interned at DeepMind with John Jumper and the AlphaFold team and previously worked on molecular dynamics algorithms and infrastructure for drug discovery at D. E. Shaw Research. She obtained her B.S. from the University of Virginia where she worked with Michael Shirts on computational methods for studying protein folding.

For more information about her research and group, please visit her group website: https://ezlab.princeton.edu/