The purpose of this nonprofit site, named VIRIONS, is to open the files (programs, data, manuals, and theoretical documents) written by Shigetaka Yoneda, Professor Emeritus, Kitasato University. SY hopes that the files would help theoretical analysis and modeling of virus particles (virions). The site was founded in January 2022 and the construction is still continuing.

A large part of VIRIONS will be related with the CAPLIB library in GitHub (https://github.com/picorna/caplib). Whereas programs are uploaded to CAPLIB, documents and manuals will be uploaded herein.

S. Yoneda is a computational physicist in the field of biophysics. The final two articles in the following list are closely related with VIRIONS.

• S. Yoneda, “Correlated Variations of Bond Lengths in Pseudorotating Furanose Rings”, J. Biomole. Struct. Dyn. 7, 723-738, 1989.
• S. Yoneda, K. Kitamura, M. Doi, M. Inoue, T. Ishida, “Importance of Folded Monomer and Extended Antiparallel Dimer Structures as Enkephalin Active Conformation”, FEBS Letters 239, 271-275, 1988.
• S. Yoneda, H. Umeyama, “Free Energy Perturbation Calculations on Multiple Mutation Bases”, J. Chem. Phys. 97, 6730-6736, 1992.
• S. Yoneda, M. Kitazawa, H. Umeyama, “Molecular Dynamics Simulation of a Rhinoviral Capsid under Rotational Symmetry Boundary Conditions”, J. Comput. Chem. 17, 191-203, 1996.
• S. Yoneda, Y. Hara-Yamada, A. Kosugi, M. Nanao, T. Saito, S. Sato, N. Yamada, G. Watanabe, “CAPLIB: A New Program Library for the Modeling and Analysis of Icosahedrally Symmetric Viral Capsids”, ACS Omega 3, 4458, 2018.

Shigetaka Yoneda at VIRIONS Labo, 2023.