2009 |
8 | EE | Yuto Komeiji,
Takeshi Ishikawa,
Yuji Mochizuki,
Hiroshi Yamataka,
Tatsuya Nakano:
Fragment Molecular Orbital method-based Molecular Dynamics (FMO-MD) as a simulator for chemical reactions in explicit solvation.
Journal of Computational Chemistry 30(1): 40-50 (2009) |
2008 |
7 | EE | Bryan M. B. VanSchouwen,
Heather L. Gordon,
Stuart M. Rothstein,
Yuto Komeiji,
Kaori Fukuzawa,
Shigenori Tanaka:
Water-mediated interactions in the CRP-cAMP-DNA complex: Does water mediate sequence-specific binding at the DNA primary-kink site?
Computational Biology and Chemistry 32(3): 149-158 (2008) |
2007 |
6 | EE | Yuto Komeiji,
Toyokazu Ishida,
Dmitri G. Fedorov,
Kazuo Kitaura:
Change in a protein's electronic structure induced by an explicit solvent: An ab initio fragment molecular orbital study of ubiquitin.
Journal of Computational Chemistry 28(10): 1750-1762 (2007) |
5 | EE | Kaori Fukuzawa,
Yuto Komeiji,
Yuji Mochizuki,
Akifumi Kato,
Tatsuya Nakano,
Shigenori Tanaka:
Intra- and intermolecular interactions between cyclic-AMP receptor protein and DNA: Ab initio fragment molecular orbital study.
Journal of Computational Chemistry 28(13): 2237-2239 (2007) |
2006 |
4 | EE | Kaori Fukuzawa,
Yuto Komeiji,
Yuji Mochizuki,
Akifumi Kato,
Tatsuya Nakano,
Shigenori Tanaka:
Intra- and intermolecular interactions between cyclic-AMP receptor protein and DNA: Ab initio fragment molecular orbital study.
Journal of Computational Chemistry 27(8): 948-960 (2006) |
2005 |
3 | EE | Tadashi Nemoto,
Dmitri G. Fedorov,
Masami Uebayasi,
Kenji Kanazawa,
Kazuo Kitaura,
Yuto Komeiji:
Ab initio fragment molecular orbital (FMO) method applied to analysis of the ligand-protein interaction in a pheromone-binding protein.
Computational Biology and Chemistry 29(6): 434-439 (2005) |
2001 |
2 | | Yuto Komeiji,
Makoto Haraguchi,
Umpei Nagashima:
Parallel molecular dynamics simulation of a protein.
Parallel Computing 27(8): 977-987 (2001) |
1997 |
1 | EE | Yuto Komeiji,
Masami Uebayasi,
Ryo Takata,
Akihiro Shimizu,
Keiji Itsukashi,
Makoto Taiji:
Fast and accurate molecular dynamics simulation of a protein using a special-purpose computer.
Journal of Computational Chemistry 18(12): 1546-1563 (1997) |