Rigid-body dynamics in the isothermal-isobaric ensemble: A test on the accuracy and computational efficiency. - Wataru Shinoda; Masuhiro Mikami (J. Comput. Chem., 2003)

Efficient free energy calculation of water across lipid membranes. - Keiko Shinoda; Wataru Shinoda; Masuhiro Mikami (J. Comput. Chem., 2008)

Precise calculation of the local pressure tensor in Cartesian and spherical coordinates in LAMMPS. - Takenobu Nakamura; Shuhei Kawamoto; Wataru Shinoda (Comput. Phys. Commun., 2015)

Identification of Factors Promoting HBV Capsid Self-Assembly by Assembly-Promoting Antivirals. - Soumya Lipsa Rath; Huihui Liu; Susumu Okazaki; Wataru Shinoda (J. Chem. Inf. Model., 2018)

Development of dissociative force field for all-atomistic molecular dynamics calculation of fracture of polymers. - Kazushi Fujimoto; Rajadeep Singh Payal; Tomonori Hattori; Wataru Shinoda; Masayuki Nakagaki; Shigeyoshi Sakaki; Susumu Okazaki (J. Comput. Chem., 2019)

tSPICA: Temperature- and Pressure-Dependent Coarse-Grained Force Field for Organic Molecules. - Mark Z. Griffiths; Wataru Shinoda (J. Chem. Inf. Model., 2019)

Heteroaryldihydropyrimidines Alter Capsid Assembly By Adjusting the Binding Affinity and Pattern of the Hepatitis B Virus Core Protein. - Huihui Liu; Susumu Okazaki; Wataru Shinoda (J. Chem. Inf. Model., 2019)

pSPICA Force Field Extended for Proteins and Peptides. - Yusuke Miyazaki 004; Wataru Shinoda (J. Chem. Inf. Model., 2024)