Simulated tempering based on global balance or detailed balance conditions: Suwa-Todo, heat bath, and Metropolis algorithms. - Yoshiharu Mori; Hisashi Okumura (J. Comput. Chem., 2015)

Conformational changes of ubiquitin under high pressure conditions: A pressure simulated tempering molecular dynamics study. - Yoshiharu Mori; Yuko Okamoto (J. Comput. Chem., 2017)

Thermal conductivity and conductance of protein in aqueous solution: Effects of geometrical shape. - Ikuo Kurisaki; Seiya Tanaka; Ichiro Mori; Toshihito Umegaki; Yoshiharu Mori; Shigenori Tanaka (J. Comput. Chem., 2023)

End-to-end protein-ligand complex structure generation with diffusion-based generative models. - Shuya Nakata; Yoshiharu Mori; Shigenori Tanaka (BMC Bioinform., 2023)

Navigating Ultralarge Virtual Chemical Spaces with Product-of-Experts Chemical Language Models. - Shuya Nakata; Yoshiharu Mori; Shigenori Tanaka (J. Chem. Inf. Model., 2024)