Yuto Komeiji - researchr alias

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Viewing Publication 1 - 9 from 9

2020

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. jcisd, 60(7):3593-3602, 2020. [doi]

2009

Fragment Molecular Orbital method-based Molecular Dynamics (FMO-MD) as a simulator for chemical reactions in explicit solvationYuto Komeiji, Takeshi Ishikawa, Yuji Mochizuki, Hiroshi Yamataka, Tatsuya Nakano. jcc, 30(1):40-50, 2009. [doi]

2008

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. CANDC, 32(3):149-158, 2008. [doi]

2007

Intra- and intermolecular interactions between cyclic-AMP receptor protein and DNA: Ab ::::initio:::: fragment molecular orbital studyKaori Fukuzawa, Yuto Komeiji, Yuji Mochizuki, Akifumi Kato, Tatsuya Nakano, Shigenori Tanaka. jcc, 28(13):2237-2239, 2007. [doi]

Change in a protein s electronic structure induced by an explicit solvent: An ::::ab initio:::: fragment molecular orbital study of ubiquitinYuto Komeiji, Toyokazu Ishida, Dmitri G. Fedorov, Kazuo Kitaura. jcc, 28(10):1750-1762, 2007. [doi]

2006

Intra- and intermolecular interactions between cyclic-AMP receptor protein and DNA: Ab initio fragment molecular orbital studyKaori Fukuzawa, Yuto Komeiji, Yuji Mochizuki, Akifumi Kato, Tatsuya Nakano, Shigenori Tanaka. jcc, 27(8):948-960, 2006. [doi]

2005

Ab initio fragment molecular orbital (FMO) method applied to analysis of the ligand-protein interaction in a pheromone-binding proteinTadashi Nemoto, Dmitri G. Fedorov, Masami Uebayasi, Kenji Kanazawa, Kazuo Kitaura, Yuto Komeiji. CANDC, 29(6):434-439, 2005. [doi]

2001

Parallel molecular dynamics simulation of a proteinYuto Komeiji, Makoto Haraguchi, Umpei Nagashima. pc, 27(8):977-987, 2001.

1997

Fast and accurate molecular dynamics simulation of a protein using a special-purpose computerYuto Komeiji, Masami Uebayasi, Ryo Takata, Akihiro Shimizu, Keiji Itsukashi, Makoto Taiji. jcc, 18(12):1546-1563, 1997. [doi]

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