Fast and accurate molecular dynamics simulation of a protein using a special-purpose computer. - Yuto Komeiji; Masami Uebayasi; Ryo Takata; Akihiro Shimizu; Keiji Itsukashi; Makoto Taiji (J. Comput. Chem., 1997)

Parallel molecular dynamics simulation of a protein. - Yuto Komeiji; Makoto Haraguchi; Umpei Nagashima (Parallel Comput., 2001)

Ab initio fragment molecular orbital (FMO) method applied to analysis of the ligand-protein interaction in a pheromone-binding protein. - Tadashi Nemoto; Dmitri G. Fedorov; Masami Uebayasi; Kenji Kanazawa; Kazuo Kitaura; Yuto Komeiji (Comput. Biol. Chem., 2005)

Intra- and intermolecular interactions between cyclic-AMP receptor protein and DNA: Ab initio fragment molecular orbital study. - Kaori Fukuzawa; Yuto Komeiji; Yuji Mochizuki; Akifumi Kato; Tatsuya Nakano; Shigenori Tanaka (J. Comput. Chem., 2006)

Intra- and intermolecular interactions between cyclic-AMP receptor protein and DNA: Ab initio fragment molecular orbital study. - Kaori Fukuzawa; Yuto Komeiji; Yuji Mochizuki; Akifumi Kato; Tatsuya Nakano; Shigenori Tanaka (J. Comput. Chem., 2007)

Change in a protein's electronic structure induced by an explicit solvent: An ab initio fragment molecular orbital study of ubiquitin. - Yuto Komeiji; Toyokazu Ishida; Dmitri G. Fedorov; Kazuo Kitaura (J. Comput. Chem., 2007)

Water-mediated interactions in the CRP-cAMP-DNA complex: Does water mediate sequence-specific binding at the DNA primary-kink site? - Bryan M. B. VanSchouwen; Heather L. Gordon; Stuart M. Rothstein; Yuto Komeiji; Kaori Fukuzawa; Shigenori Tanaka (Comput. Biol. Chem., 2008)

Fragment Molecular Orbital method-based Molecular Dynamics (FMO-MD) as a simulator for chemical reactions in explicit solvation. - Yuto Komeiji; Takeshi Ishikawa; Yuji Mochizuki; Hiroshi Yamataka; Tatsuya Nakano (J. Comput. Chem., 2009)

Fragment Molecular Orbital Based Interaction Analyses on COVID-19 Main Protease - Inhibitor N3 Complex (PDB ID: 6LU7). - Ryo Hatada; Koji Okuwaki; Yuji Mochizuki; Yuma Handa; Kaori Fukuzawa; Yuto Komeiji; Yoshio Okiyama; Shigenori Tanaka (J. Chem. Inf. Model., 2020)