Improvement of User Interface for Blind PC Users. - Yutaka Shimizu; Masami Shinohara; Hideji Nagaoka; Yasushige Yonezawa (ICCHP, 2002)

Application of MDGRAPE-3, a special purpose board for molecular dynamics simulations, to periodic biomolecular systems. - Gota Kikugawa; Rossen Apostolov; Narutoshi Kamiya; Makoto Taiji; Ryutaro Himeno; Haruki Nakamura; Yasushige Yonezawa (J. Comput. Chem., 2009)

Effective Computational Method for Evaluation of Dynamic Elecrostatic Effects of Explicit Solvent and Membrane Molecules from Molecular Dynamics Simulations. - Yasushige Yonezawa (e-Science Workshops, 2011)

Theory for trivial trajectory parallelization of multicanonical molecular dynamics and application to a polypeptide in water. - Jinzen Ikebe; Koji Umezawa; Narutoshi Kamiya; Takanori Sugihara; Yasushige Yonezawa; Yu Takano; Haruki Nakamura; Junichi Higo (J. Comput. Chem., 2011)

Development of massive multilevel molecular dynamics simulation program, platypus (PLATform for dYnamic protein unified simulation), for the elucidation of protein functions. - Yu Takano; Kazuto Nakata; Yasushige Yonezawa; Haruki Nakamura (J. Comput. Chem., 2016)

A method for predicting protein conformational pathways by using molecular dynamics simulations guided by difference distance matrices. - Yasushige Yonezawa (J. Comput. Chem., 2016)

Autoencoder-Based Detection of Dynamic Allostery Triggered by Ligand Binding Based on Molecular Dynamics. - Yuko Tsuchiya; Kei Taneishi; Yasushige Yonezawa (J. Chem. Inf. Model., 2019)

Atomistic detailed free-energy landscape of intrinsically disordered protein studied by multi-scale divide-and-conquer molecular dynamics simulation. - Hiromitsu Shimoyama; Yasushige Yonezawa (J. Comput. Chem., 2021)