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Publication

2024


Explicit description of viral capsid subunit shapes by unfolding dihedrons

Our collaborative paper with Dr. Tachi (University of Tokyo), Toyooka-san, Nishimoto-san, Tendo-san, and Dr. Horiyama (Hokkaido University) on viral capsid structure tiling has been published in Communications Biology.

Virus capsid structures are formed by proteins of the same shape assembling into icosahedra, but the possible tile shapes were not well understood. Through this collaboration with the Tachi group and Dr. Horiyama, who are experts in tiling, we developed a framework to explicitly describe capsid tile shapes and applied it to classify actual viral capsid structures.

2020


Publications

Papers #

  • R. Toyooka, S. Nishimoto, T. Tendo, T. Horiyama*, T. Tachi*, and Y. Matsunaga*, “Explicit description of viral capsid subunit shapes by unfolding dihedrons” Communications Biology 7, 1509 (9 pages) (2024) DOI:10.1038/s42003-024-07218-x

  • J. Jung, K. Yagi, C. Tan, H. Oshima, T. Mori, I. Yu, Y. Matsunaga, C. Kobayashi, S. Ito, D. Ugarte La Torre, and Y. Sugita* “GENESIS 2.1: High-Performance Molecular Dynamics Software for Enhanced Sampling and Free-Energy Calculations for Atomistic, Coarse-Grained, and Quantum Mechanics/Molecular Mechanics Models” Journal of Physical Chemistry B 128, 6028-6048 (2024) DOI:10.1021/acs.jpcb.4c02096