Detection of archaeal-and prokaryotic-like ribosome exit tunnels within eukaryotic kingdoms

Yu Shiqi, Kushner Artem, Srebnik Simcha, Dao Duc Khanh (2025). Biophysical Journal

Advanced coarse-grained model for fast simulation of nascent polypeptide chain dynamics within the ribosome

Shiqi Yu, Artem Kushner, Ella Teasell, Wenjun Zhao, Simcha Srebnik, Khanh Dao Duc (2025). Biophysical Journal

We present an advanced coarse-grained model for simulating the dynamics of nascent polypeptide chains within the ribosome

RiboXYZ: a comprehensive database for visualizing and analyzing ribosome structures

Artem Kushner, Anton S. Petrov, and Khanh Dao Duc (2023). Nucleic Acids Research

RiboXYZ is a comprehensive database designed for the visualization and analysis of ribosome structures from various organisms and functional states. Visit the project at ribosome.xyz.

Application of transport-based metric for continuous interpolation between cryo-EM density maps

Arthur Ecoffet, Geoffrey Woollard, Artem Kushner, Frédéric Poitevin, Khanh Dao Duc (2022). AIMS Mathematics

We present an approach to interpolating between cryo-EM density maps based on the theory of optimal transport, allowing for a more physically meaningful representation of conformational changes.

Structural heterogeneities of the ribosome: new frontiers and opportunities for cryo-EM

Frédéric Poitevin, Artem Kushner, Xinpei Li, and Khanh Dao Duc (2020). Molecules

This paper explores the structural heterogeneities of the ribosome across evolutionary, cellular, temporal and conformational landscapes, highlighting new frontiers for cryo-EM.

Computational methods for unraveling ribosome structural heterogeneity

Artem Kushner, Shiqi Yu, Aryan Tajmir Riahi, and Simcha Srebnik, Khanh Dao Duc (2023). Royal Society: Ribosome Heterogeneity and Specialisation Workshop

We shared some computational methods for analyzing ribosome structural heterogeneity.