On easy implementation of a variant of the replica exchange with solute tempering in GROMACS. - Tsuyoshi Terakawa; Tomoshi Kameda; Shoji Takada (J. Comput. Chem., 2011)

Modeling of DNA binding to the condensin hinge domain using molecular dynamics simulations guided by atomic force microscopy. - Hiroki Koide; Noriyuki Kodera; Shveta Bisht; Shoji Takada; Tsuyoshi Terakawa (PLoS Comput. Biol., 2021)

Molecular dynamics simulations of human cohesin subunits identify DNA binding sites and their potential roles in DNA loop extrusion. - Chenyang Gu; Shoji Takada; Giovanni B. Brandani; Tsuyoshi Terakawa (PLoS Comput. Biol., 2025)