Development of DMD Reflection-Type CCD Camera for Phase Analysis and Shape Measurement. - Shien Ri; Yasuhiro Matsunaga; Motoharu Fujigaki; Toru Matui; Yoshiharu Morimoto (J. Robotics Mechatronics, 2006)

Minimum Free Energy Path of Ligand-Induced Transition in Adenylate Kinase. - Yasuhiro Matsunaga; Hiroshi Fujisaki; Tohru Terada; Tadaomi Furuta; Kei Moritsugu; Akinori Kidera (PLoS Comput. Biol., 2012)

GENESIS 1.1: A hybrid-parallel molecular dynamics simulator with enhanced sampling algorithms on multiple computational platforms. - Chigusa Kobayashi; Jaewoon Jung; Yasuhiro Matsunaga; Takaharu Mori; Tadashi Ando; Koichi Tamura; Motoshi Kamiya; Yuji Sugita (J. Comput. Chem., 2017)

Automated Planning of System Rollback in Declarative IT System Update. - Takuya Kuwahara; Takayuki Kuroda; Manabu Nakanoya; Yutaka Yakuwa; Yoichi Sato; Yasuhiro Matsunaga (IM, 2019)

Coarse-Grained Modeling of Multiple Pathways in Conformational Transitions of Multi-Domain Proteins. - Ai Shinobu; Chigusa Kobayashi; Yasuhiro Matsunaga; Yuji Sugita (J. Chem. Inf. Model., 2021)

Rigid-body fitting to atomic force microscopy images for inferring probe shape and biomolecular structure. - Toru Niina; Yasuhiro Matsunaga; Shoji Takada (PLoS Comput. Biol., 2021)

Development of hidden Markov modeling method for molecular orientations and structure estimation from high-speed atomic force microscopy time-series images. - Tomonori Ogane; Daisuke Noshiro; Toshio Ando; Atsuko Yamashita; Yuji Sugita; Yasuhiro Matsunaga (PLoS Comput. Biol., 2022)