YUTO KOMEIJI'S LIST OF PUBLICATIONS IN ENGLISH
PUBLICATIONS IN ENGLISH
Book chapters
- Komeiji, Y. Mochizuki, Y., Nakano, T., Mori, H. (2012) in "Molecular Dynamics -
Theoretical Developments and Applications in Nanotechnology and Energy (Wang, L., ed.),"
InTech, Rijeka, Kroatia.
Chapter 1: Recent advances in fragment molecular orbital-based
molecular dynamics (FMO-MD) simulations.
[Open Access Book]
- Komeiji, Y. (2009) in "The Fragment Molecular Orbital method: practical
applications to large molecular systems
(Fedorov, D. G. & Kitaura, K, eds.)," pp. 119-132, CRC Press, London.
Chapter 6 FMO-MD: An ab initio-based molecular dynamics of large systems.
[Amazon]
- Komeiji, Y. (2001) In "Recent Research Developments in Protein Engineering 1," pp. 1-20, Research Signpost, India.
Biomolecular simulation using the PEACH software.
Refereed papers, proceedings, and reviews
- Mori, H., Hirayama, N., Komeiji, Y., Y. Mochizuki (2012)
Comput. Theor. Chem. 986, 30-34.
Differences in hydration between cis- and trans-platin: Quantum insights by
ab initio fragment molecular orbital-based molecular dynamics (FMO-MD).
- Mochizuki, Y., Nakano, T., Komeiji, Y., Yamashita, K., Okiyama, Y.,
Yoshikawa, H., Yamataka, H. (2011)
Chem. Phys. Lett. 504, 95-99.
Fragment molecular orbital-based molecular dynamics (FMO-MD) method
with MP2 gradient.
- Sato, M., Yamataka, H., Komeiji, Y., Nakano, T., Mochizuki, Y. (2010)
Chem. Eur. J. 16, 6430-6433.
Does Amination of Formaldehyde Proceeds through Zwitterionic Intermediate in
Water? FMO-MD Simulations by using Constraint Dynamics.
- Fujiwara, T., Mochizuki, Y., Komeiji, Y., Okiyama, Y., Mori, H., Nakano, T.,
Miyoshi, E. (2010)
Chem. Phys. Lett. 490, 41-45.
Fragment molecular orbital-based molecular dynamics (FMO-MD) simulations
on hydrated Zn(II) ion.
- Komeiji, Y., Mochizuki, Y., Nakano, T.
(2010)
Chem. Phys. Lett. 484, 380-386.
Three-body expansion and generalized dynamic fragmentation
improve the Fragment Molecular Orbital-based Molecular Dynamics (FMO-MD).
- Komeiji, Y., Mochizuki, Y., Nakano, T., Fedorov, D. G.
(2009)
J. Mol. Struct.: THEOCHEM 898, 2-7.
Fragment Molecular Orbital-based Molecular Dynamics (FMO-MD),
a quantum simulation tool for large molecular systems.
- Komeiji, Y., Ishikawa, T., Mochizuki, Y., Yamataka, H., Nakano, T.
(2009)
J. Comput. Chem. 30, 40-50.
Fragment Molecular Orbital method-based Molecular Dynamics (FMO-MD)
as a simulator for chemical reactions in explicit solvation.
- VanSchouwen, B. M. B., Gordon, H. L., Rothstein, S. M., Komeiji, Y.,
Fukuzawa, K., Tanaka, S.
Nakano, T. (2008)
Comput. Biol. Chem. 32, 149-158.
Water-Mediated Interactions in the CRP-cAMP-DNA Complex:
Does water mediate sequence-specific binding at the DNA primary-kink site?
- Sato, M., Yamataka, H., Komeiji, Y., Mochizuki, Y., Ishikawa, T.,
Nakano, T. (2008)
J. Am. Chem. Soc., 130, 2396-2397.
How does an SN2 reaction take place in solution? Full Ab initio MD simulations
for the hydrolysis of the methyl diazonium ion.
- Komeiji, Y., Ishikawa, T., Mochizuki, Y., Yamataka, H., Nakano, T. (2007)
In "Computation in Modern Science and Engineering Vol. 2, Part B
- Proc. ICCMSE2007 (Simos, T. E, Maroulis, G., eds, AIP)," pp. 1261-1264.
Ab initio FMO-MD method reimplemented and applied to pure water.
- Komeiji, Y. (2007)
CBI J. 7, 12-23.
Implementation of the blue moon ensemble method.
- Kurisaki, I., Fukuzawa, K., Komeiji, Y., Mochizuki, Y.,
Nakano, T., Imada, J., Chmielewski, A., Rothstein, S. M.,
Watanabe, H., Tanaka, S. (2007)
Biophys. Chem. 130, 1-9.
Visualization analysis of inter-fragment interaction energies of
CRP-cAMP-DNA complex based on the fragment molecular orbital method.
- Komeiji, Y., Ishida, T., Fedorov, D. G., Kitaura, K.
(2007)
J. Comput. Chem. 28, 1750-1762.
Change in a protein's electronic structure induced by an explicit solvent:
an ab initio Fragment Molecular Orbital (FMO) study of ubiquitin.
- Mochizuki, Y., Komeiji, Y., Ishikawa, T., Nakano, T., Yamataka, H.
(2007)
Chem. Phys. Lett. 437, 66-72.
A fully quantum mechanical simulation study on the lowest n-pi*
state of hydrated formaldehyde.
- Ishikawa, T., Mochizuki, Y., Nakano, T., Amari, S., Mori, H., Honda, H., Fujita, T.,
Tokiwa, H., Tanaka, S., Komeiji, Y., Fukuzawa, K., Tanaka, K., Miyoshi, E.
(2006)
Chem. Phys. Lett. 427, 159-165.
Fragment molecular orbital calculations on large scale systems containing heavy
metal atoms.
- Fukuzawa, K., Komeiji, Y., Mochizuki, Y., Kato, A., Nakano, T.,
Tanaka, S. (2006)
J. Comput. Chem., 28, 948-960.
Intra- and intermolecular interactions between cyclic-AMP receptor protein and DNA:
Ab initio fragment molecular orbital study.
- Nemoto, T., Fedorov, D. G., Uebayasi, M., Kanazawa, K.,
Kitaura, K., Komeiji, Y. (2005)
Comput. Biol. Chem., 29, 434-439.
Ab initio fragment molecular orbital (FMO) method applied to analysis
of the ligand-protein interaction in a pheromone-binding protein.
- Komeiji, Y., Inadomi, Y., Nakano, T. (2004)
Comput. Biol. Chem., 28, 155-161.
PEACH 4 with ABINIT-MP:
a general platform for classical and quantum simulations of biological molecules.
- Komeiji, Y., Nakano, T., Fukuzawa, K., Ueno, Y.,
Inadomi, Y., Nemoto, T., Uebayasi, M., Fedorov, D. G., Kitaura, K. (2003)
Chem. Phys. Lett. 372, 342-347.
Fragment molecular orbital method:
application to molecular dynamics simulation, "ab initio FMO-MD."
- Komeiji, Y., Uebayasi, M. (2002)
CBI J. 2, 102-118.
Peach-Grape system - a high performance simulator for
biomolecules.
- Komeiji, Y., Ueno, Y., Uebayasi, M. (2002) FEBS Lett.,
521, 133-139.
Molecular dynamics simulations revealed Ca2+-dependent
conformational change of Calmodulin.
- Nemoto, T., Uebayasi, M., Komeiji, Y. (2002)
CBI J. 2, 32-37.
Flexibility of a loop in a pheromone binding protein from Bombyx mori:
a molecular dynamics simulation.
- Komeiji, Y., Haraguchi, M., Nagashima, U. (2001) Parallel Computing
27, 977-987.
Parallel molecular dynamics simulation of a protein.
- Kitaura, K., Sugiki, S., Nakano, T., Komeiji, Y., Uebayasi, M.,
(2001) Chem. Phys. Lett. 336, 163-170.
Fragment molecular orbital method: analytical energy gradients.
- Komeiji, Y. (2001) In "Proceedings of Sixth International Symposium
on Artificial Life and Robotics (AROB 6th'01)," pp. 349-352.
Interaction mechanism between DNA and substrate clarified based
on molecular dynamics.
- Komeiji, Y. (2000) J. Mol. Struct.: THEOCHEM,
530, 237-243.
Ewald summation and multiple time step methods for
molecular dynamics simulation of biological molecules.
- Suenaga, A., Yatsu, C., Komeiji, Y., Uebayasi, M.,
Meguro, T., Yamato, I. (2000) J. Mol. Struct.
526, 209-218.
Molecular dynamics simulation of trp-repressor/operator complex:
analysis of hydrogen bond patterns of protein-DNA interaction.
- Komeiji, Y., Harata, K., Ueno, Y., Uebayasi, M. (2000)
JCPE J. 12, 39-48.
Anisotropic motion within a protein: comparison between
X-ray crystallography and molecular dynamics simulation
of Human Lysozyme.
- Komeiji, Y., Uebayasi, M. (1999) Biophys. J. 77, 123-138.
Change in conformation by DNA-peptide association:
Molecular dynamics of the Hin-recombinase-hixL complex.
- Komeiji, Y., Uebayasi, M. (1999) Mol. Simul. 21, 303-324.
Molecular Dynamics Simulation of the Hin-Recombinase-DNA Complex.
- Taira, K., Kuwabara, T., Warashina, M, Nakayama, A., Hamada, M.,
Amontov, S., Takasuka, Y., Komeiji, Y. (1998)
Gene Therapy and Molecular Biology 1, 435-449.
Comparison of the Specificities and Catalytic Activities of
Conventional Hammerhead Ribozymes, Joyce's DNA Enzymes,
and Novel Dimeric Minizymes with Respect to the cleavage of
BCR-ABL Chimeric L6 (b2a2) mRNA.
- Suenaga, A., Komeiji, Y., Uebayasi, M., Meguro, T., Saito, M.,
Yamato, I. (1998) Biosci. Rep. 18, 39-48.
Computational observation of an ion permeation through a channel protein.
- Suenaga, A., Komeiji, Y., Uebayasi, M., Meguro, T., Yamato, I. (1998)
J. Chem. Software 4, 127-142.
Molecular dynamics simulation of unfolding of histidine-containing
phosphocarrier protein in water
- Komeiji, Y., Uebayasi, M., Takata, R., Shimizu, A., Itsukashi, K,
Taiji, M. (1997) J. Comput. Chem. 18, 1546-1563.
Fast and accurate molecular dynamics simulation of a protein using a
special purpose computer.
- Honda, N., Komeiji, Y., Uebayasi, M., Yamato, I. (1996) Proteins 26,
459-464.
Computational design of a substrate specificity mutant of a protein.
- Komeiji, Y., Yokoyama, H., Uebayasi, M. Taiji, M. Fukushige, T.,
Sugimoto, D., Takata, R., Shimizu, A., Itsukashi, K. (1996)
In "Pacific Symposium on Biocomputing '96 (Hunter & Klein eds.,
World Scientific)," pp. 472-487.
A High performance system for molecular dynamics simulation of
biomolecules using a special-purpose computer.
- Fujita, I., Komeiji, Y., Yamato, I. (1995) Protein Engng. 8, 935-938.
Threonine 81 of the trp-repressor of E. coli plays an auxiliary role
for the formation of the corepressor binding pocket.
- Komeiji, Y., Uebayasi, M., Yamato, I. (1994) Proteins 30, 248-258.
Molecular dynamics simulations of the trp apo- and holo-repressors:
domain structure and ligand-protein interaction.
- Komeiji, Y., Fujita, I., Honda, N., Tsutsui, M., Tamura, T., Yamato, I.
(1994) Protein Engng.7, 1239-1247.
Glycine-85 of the trp-Repressor of E. coli is important in forming the
hydrophobic tryptophan binding pocket.
- Komeiji, Y., Honda, N., Yamato, I. (1993) Biophys. Chem. 47, 113-121.
Helix propensity of Ala and Val: A free energy perturbation study.
- Komeiji, Y., Uebayasi, M. Someya, J., Yamato, I. (1993) Proteins 16,
268-277.
A molecular dynamics study of solvent behavior around a protein.
- Komeiji, Y., Uebayasi, M. Someya, J., Yamato, I. (1992)
Protein Engng. 5, 759-767.
Free energy perturbation study on a Trp-binding mutant (Ser88->Cys) of
the trp-repressor.
- Komeiji, Y., Uebayasi, M. Someya, J., Yamato, I. (1991)
Protein Engng. 4, 871-875.
Molecular dynamics simulation of trp-aporepressor in a solvent.
- Komeiji, Y., Hanada, K., Yamato, I., Anraku, Y. (1989)
FEBS Lett. 256, 135-138.
Orientation of the carboxyl teminus of the Na+/proline symport
carrier in Escherichia coli.
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