The One World Cryo-EM seminar series is a platform for discussion of algorithms, computational methods and mathematical problems in cryo-EM.

Online, Every Other Wednesday, at 8am PT / 11am ET/ 4pm BST / 5pm CET / 11pm China.

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Organizers: Joakim Andén, Dorit Hanein, Roy R. Lederman and Steven J. Ludtke

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Next Talk

Yuntao Liu

Postdoctoral scholar, California NanoSystems Institute, UCLA

Date and time: Apr 10th, 2024
Wednesday, at 8am PST / 11am EDT / 3pm GMT / 5pm CET / 11pm China

For the zoom and links, please join the One World Cryo-EM mailing list.

Single-particle IsoNet: an AI-based method to overcome the “preferred” orientation problem

While advances in single-particle cryoEM have enabled the structural determination of macromolecular complexes at atomic resolution, particle orientation bias (the so-called “preferred” orientation problem) remains a complication for most specimens. Existing solutions have relied on biochemical and physical strategies applied to the specimen and are often complex and challenging. Here, we develop spIsoNet, an end-to-end self-supervised deep-learning software to address the preferred orientation problem. Using preferred-orientation views to recover molecular information in under-sampled views, spIsoNet improves both angular isotropy and particle alignment accuracy during 3D reconstruction. We demonstrate spIsoNet’s capability of generating near-isotropic reconstructions from representative biological systems with limited views, including ribosomes, β-galactosidases, and a previously intractable hemagglutinin trimer dataset. spIsoNet can also be generalized to improve map isotropy and particle alignment of preferentially oriented molecules in subtomogram averaging. Therefore, without additional specimen-preparation procedures, spIsoNet provides a general computational solution to the preferred orientation problem. 

Last Talk

Quanquan Gu

Head of AI for Drug Design, ByteDance Research

Date and time: Mar 6th, 2024
Wednesday, at 8am PST / 11am EST / 4pm GMT / 5pm CET / 12am China

For the zoom and links, please join the One World Cryo-EM mailing list.

CryoSTAR: Leveraging Structural Prior and Constraints for Cryo-EM Heterogeneous Reconstruction

Resolving conformational heterogeneity in cryo-electron microscopy (cryo-EM) datasets remains a significant challenge in structural biology. Previous methods have often been restricted to working exclusively on volumetric densities, neglecting the potential of incorporating any pre-existing structural knowledge as prior or constraints. In this talk, I will present a novel methodology, cryoSTAR, that harnesses atomic model information as structural regularization to elucidate such heterogeneity. Our method uniquely outputs both coarse-grained models and density maps, showcasing the molecular conformational changes at different levels. Validated against four diverse experimental datasets, spanning large complexes, a membrane protein, and a small single-chain protein, our results consistently demonstrate an efficient and effective solution to conformational heterogeneity with minimal human bias. By integrating atomic model insights with cryo-EM data, cryoSTAR represents a meaningful step forward, paving the way for a deeper understanding of dynamic biological processes. This is joint work with Yilai Li, Yi Zhou, Jing Yuan and Fei Ye.

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