Personal information

Emails & domains

Verified email domains

Websites & social links

Yuto Komeiji @ researchmap

Other IDs

Scopus Author ID: 6701563580
ResearcherID: L-7992-2018

Keywords

simulation, MD, FMO, FMO-MD, protein, DNA, Programming, Kyudo

Countries

Japan

Activities

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Employment (7)

Osaka University: Osaka, Osaka, JP

2025-04-01 to present | Guest Professor (School of Pharmaceutical Sciences)
Employment
Source: Self-asserted source
Yuto Komeiji

Rikkyo University: Tokyo, JP

2008-04-01 to present | Part-time lecturer (Chemistry)
Employment
Source: Self-asserted source
Yuto Komeiji

National Institute of Advanced Industrial Science and Technology (AIST): Tsukuba, Ibaraki, JP

1992-04-01 to present | Senior Staff (since Apr. 2025)
Employment
Source: Self-asserted source
Yuto Komeiji

Osaka University: Osaka, Osaka, JP

2023-04-01 to 2025-03-31 | Visiting academic staff (Graduate school of pharmaceutical sciences)
Employment
Source: Self-asserted source
Yuto Komeiji

Rikkyo University: Tokyo, JP

2011-04-01 to 2025-03-31 | Guest professor (Chemistry)
Employment
Source: Self-asserted source
Yuto Komeiji

Saitama University: Saitama, Saitama, JP

2022-04-01 to 2024-09-30 | Part-time lecturer (Department of applied chemistry)
Employment
Source: Self-asserted source
Yuto Komeiji

RIKEN Yokohama JP: Yokohama, Kanagawa, JP

2019-12-01 to 2024-03-31 | Guest Researcher (Center for Biosystems Dynamics Research)
Employment
Source: Self-asserted source
Yuto Komeiji

Education and qualifications (4)

University of Tokyo: Tokyo, JP

1989-04-01 to 1992-03-31 | Ph D (Botany)
Education
Source: Self-asserted source
Yuto Komeiji

University of Tokyo: Tokyo, JP

1987-04-01 to 1989-03-31 | MS (Botany)
Education
Source: Self-asserted source
Yuto Komeiji

University of Tokyo: Tokyo, JP

1985-04-01 to 1987-03-31 | BS (Agricultural biology)
Education
Source: Self-asserted source
Yuto Komeiji

University of Tokyo: Tokyo, JP

1983-04-01 to 1985-03-31 (College of Arts and Sciences)
Education
Source: Self-asserted source
Yuto Komeiji

Professional activities (5)

Japanese Society for Extremophiles: Yokohama, JP

2015-04-01 to present
Membership
Source: Self-asserted source
Yuto Komeiji

Kyudo Specialized Committee, Japanese Academy of Budo: Katsuura, Chiba, JP

2010-04-01 to present
Membership
Source: Self-asserted source
Yuto Komeiji

The Chemo-Bio Informatics Society (CBI): Tokyo, JP

2000-04-01 to present
Membership
Source: Self-asserted source
Yuto Komeiji

Biophysical Society: Rockville, Maryland, US

1996-02-01 to present
Membership
Source: Self-asserted source
Yuto Komeiji

Molecular simulation Society of Japan: Tokyo, JP

1992-04-01 to present
Membership
Source: Self-asserted source
Yuto Komeiji

Funding (2)

Microscopic Analysis of Dynamics-Controlled Organic Reactions

2010-04-01 to 2014-03-31 | Grant
Japan Society for the Promotion of Science (Tokyo, JP)
URL: https://app.dimensions.ai/details/grant/grant.6031309
GRANT_NUMBER: 22350023
Source: Self-asserted source
Yuto Komeiji via DimensionsWizard

Electronic structure calculations on K^+ ion channel protein

2002-01-01 to 2003-12-31 | Grant
Japan Society for the Promotion of Science (Tokyo, JP)
URL: https://app.dimensions.ai/details/grant/grant.5817266
GRANT_NUMBER: 14540482
Source: Self-asserted source
Yuto Komeiji via DimensionsWizard

Works (50 of 68)

Items per page:
Page 1 of 2

Acceleration of Environmental Electrostatic Potential Using Cholesky Decomposition with Adaptive Metric (CDAM) for Fragment Molecular Orbital-based Molecular Dynamics (FMO-MD) Simulation

Journal of Computer Chemistry, Japan -International Edition
2024 | Journal article
DOI: 10.2477/jccjie.2023-0038
Part of ISSN: 2189-048X
Contributors: Tatsuya NAKANO; Yoshio OKIYAMA; Katsunori SEGAWA; Yoshiro SAITO; Yuji MOCHIZUKI; Yuto KOMEIJI
Source: Self-asserted source
Yuto Komeiji

Prediction of Binding Pose and Affinity of Nelfinavir, a SARS-CoV-2 Main Protease Repositioned Drug, by Combining Docking, Molecular Dynamics, and Fragment Molecular Orbital Calculations

The Journal of Physical Chemistry B
2024-03-14 | Journal article
DOI: 10.1021/acs.jpcb.3c05564
Part of ISSN: 1520-6106
Part of ISSN: 1520-5207
Contributors: Yuma Handa; Koji Okuwaki; Yusuke Kawashima; Ryo Hatada; Yuji Mochizuki; Yuto Komeiji; Shigenori Tanaka; Takayuki Furuishi; Etsuo Yonemochi; Teruki Honma et al.
Source: Self-asserted source
Yuto Komeiji

Thermal and Quantum Fluctuations of Harmonic Oscillator

JOURNAL OF PHYSICS AND CHEMISTRY RESEARCH
2022-12-03 | Journal article
DOI: 10.36266/jpcr/151
Source: Self-asserted source
Yuto Komeiji

Collective residue interactions in trimer complexes of SARS-CoV-2 spike proteins analyzed by fragment molecular orbital method

Applied Physics Express
2022-01-01 | Journal article
DOI: 10.35848/1882-0786/ac4300
Contributors: Koji Okuwaki; Kazuki Akisawa; Ryo Hatada; Yuji Mochizuki; Kaori Fukuzawa; Yuto Komeiji; Shigenori Tanaka
Source: check_circle
Crossref

Interaction analyses of SARS-CoV-2 spike protein based on fragment molecular orbital calculations

RSC Advances
2021 | Journal article
DOI: 10.1039/D0RA09555A
Contributors: Kazuki Akisawa; Ryo Hatada; Koji Okuwaki; Yuji Mochizuki; Kaori Fukuzawa; Yuto Komeiji; Shigenori Tanaka
Source: check_circle
Crossref

Fragment molecular orbital based interaction analyses on complexes between SARS-CoV-2 RBD variants and ACE2

Japanese Journal of Applied Physics
2021-09-01 | Journal article
DOI: 10.35848/1347-4065/ac1857
Contributors: Kazuki Akisawa; Ryo Hatada; Koji Okuwaki; Shun Kitahara; Yusuke Tachino; Yuji Mochizuki; Yuto Komeiji; Shigenori Tanaka
Source: check_circle
Crossref

Dynamic Cooperativity of Ligand–Residue Interactions Evaluated with the Fragment Molecular Orbital Method

The Journal of Physical Chemistry B
2021-06-24 | Journal article
DOI: 10.1021/acs.jpcb.1c03043
Contributors: Shigenori Tanaka; Shusuke Tokutomi; Ryo Hatada; Koji Okuwaki; Kazuki Akisawa; Kaori Fukuzawa; Yuto Komeiji; Yoshio Okiyama; Yuji Mochizuki
Source: check_circle
Crossref

Ca2+-ATPase Molecules as a Calcium-Sensitive Membrane-Endoskeleton of Sarcoplasmic Reticulum

International Journal of Molecular Sciences
2021-03-05 | Journal article
DOI: 10.3390/ijms22052624
Part of ISSN: 1422-0067
Source: Self-asserted source
Yuto Komeiji

Dynamical Cooperativity of Ligand-Residue Interactions Evaluated with the Fragment Molecular Orbital Method

2021-02-10 | Preprint
DOI: 10.26434/chemrxiv.13775182.v1
Contributors: Shigenori Tanaka; Shusuke Tokutomi; Ryo Hatada,; Koji Okuwaki; Kazuki Akisawa; Kaori Fukuzawa; Yuto Komeiji; Yoshio Okiyama; Yuji Mochizuki
Source: check_circle
Crossref

Statistical interaction analyses between SARS-CoV-2 main protease and inhibitor N3 by combining molecular dynamics simulation and fragment molecular orbital calculation

Applied Physics Express
2021-02-01 | Journal article
DOI: 10.35848/1882-0786/abdac6
Contributors: Ryo Hatada; Koji Okuwaki; Kazuki Akisawa; Yuji Mochizuki; Yuma Handa; Kaori Fukuzawa; Yuto Komeiji; Yoshio Okiyama; Shigenori Tanaka
Source: check_circle
Crossref

Acceleration of Environmental Electrostatic Potential Using Cholesky Decomposition with Adaptive Metric (CDAM) for Fragment Molecular Orbital (FMO) Method

Bulletin of the Chemical Society of Japan
2021-01-15 | Journal article
DOI: 10.1246/bcsj.20200227
Part of ISSN: 0009-2673
Part of ISSN: 1348-0634
Source: Self-asserted source
Yuto Komeiji

Fragment Molecular Orbital Based Interaction Analyses on COVID-19 Main Protease − Inhibitor N3 Complex (PDB ID: 6LU7)

Journal of Chemical Information and Modeling
2020-07-27 | Journal article
DOI: 10.1021/acs.jcim.0c00283
Part of ISSN: 1549-9596
Part of ISSN: 1549-960X
Source: Self-asserted source
Yuto Komeiji

Ab Initio Fragment Molecular Orbital-Based Molecular Dynamics (FMO-MD) Simulations of (NH3)32 Cluster: Effects of Electron Correlation

Bulletin of the Chemical Society of Japan
2020-04-15 | Journal article
DOI: 10.1246/bcsj.20190320
Part of ISSN: 0009-2673
Part of ISSN: 1348-0634
Source: Self-asserted source
Yuto Komeiji

Cm3+/Eu3+ induced structural, mechanistic and functional implications for calmodulin

Physical Chemistry Chemical Physics
2019 | Journal article
DOI: 10.1039/C9CP03750K
Contributors: Björn Drobot; Moritz Schmidt; Yuji Mochizuki; Takaya Abe; Koji Okuwaki; Florian Brulfert; Sven Falke; Sergey A. Samsonov; Yuto Komeiji; Christian Betzel et al.
Source: check_circle
Crossref

Potentiating Antigen-Specific Antibody Production with Peptides Obtained from In Silico Screening for High-Affinity against MHC-II

Molecules
2019-08-14 | Journal article
DOI: 10.3390/molecules24162949
Part of ISSN: 1420-3049
Source: Self-asserted source
Yuto Komeiji

Accuracy of dimer-es approximation on fragment molecular orbital (Fmo) method

Chem-Bio Informatics Journal
2018 | Journal article
DOI: 10.1273/cbij.18.119
EID:

2-s2.0-85055037494
Contributors: Nakano, T.; Fukuzawa, K.; Okiyama, Y.; Watanabe, C.; Komeiji, Y.; Mochizuki, Y.
Source: Self-asserted source
Yuto Komeiji via Scopus - Elsevier

Application of tensorflow to recognition of visualized results of fragment molecular orbital (FMO) calculations

Chem-Bio Informatics Journal
2018 | Journal article
DOI: 10.1273/cbij.18.58
EID:

2-s2.0-85045045263
Contributors: Saitou, S.; Iijima, J.; Fujimoto, M.; Mochizuki, Y.; Okuwaki, K.; Doi, H.; Komeiji, Y.
Source: Self-asserted source
Yuto Komeiji via Scopus - Elsevier

Interaction between a Single-Stranded DNA and a Binding Protein Viewed by the Fragment Molecular Orbital Method

Bulletin of the Chemical Society of Japan
2018 | Journal article
DOI: 10.1246/bcsj.20180150
EID:

2-s2.0-85056630548
Contributors: Komeiji, Y.; Okiyama, Y.; Mochizuki, Y.; Fukuzawa, K.
Source: Self-asserted source
Yuto Komeiji via Scopus - Elsevier

Explicit solvation of a single-stranded DNA, a binding protein, and their complex: A suitable protocol for fragment molecular orbital calculation

Chem-Bio Informatics Journal
2017 | Journal article
DOI: 10.1273/cbij.17.72
EID:

2-s2.0-85026732089
Contributors: Komeiji, Y.; Okiyama, Y.; Mochizuki, Y.; Fukuzawa, K.
Source: Self-asserted source
Yuto Komeiji via Scopus - Elsevier

Fragment molecular orbital (FMO) calculations on DNA by a scaled third-order Møller-Plesset perturbation (MP2.5) scheme

Computational and Theoretical Chemistry
2017 | Journal article
DOI: 10.1016/j.comptc.2016.12.008
EID:

2-s2.0-85007318912
Contributors: Yamada, H.; Mochizuki, Y.; Fukuzawa, K.; Okiyama, Y.; Komeiji, Y.
Source: Self-asserted source
Yuto Komeiji via Scopus - Elsevier

Hydration of ligands of influenza virus neuraminidase studied by the fragment molecular orbital method

Journal of Molecular Graphics and Modelling
2016 | Journal article
DOI: 10.1016/j.jmgm.2016.08.004
EID:

2-s2.0-84985912253
Contributors: Tokuda, K.; Watanabe, C.; Okiyama, Y.; Mochizuki, Y.; Fukuzawa, K.; Komeiji, Y.
Source: Self-asserted source
Yuto Komeiji via Scopus - Elsevier

Explicit solvation modulates intra- and inter-molecular interactions within DNA: Electronic aspects revealed by the ab initio fragment molecular orbital (FMO) method

Computational and Theoretical Chemistry
2015 | Journal article
DOI: 10.1016/j.comptc.2014.11.020
EID:

2-s2.0-84919934487
Contributors: Fukuzawa, K.; Kurisaki, I.; Watanabe, C.; Okiyama, Y.; Mochizuki, Y.; Tanaka, S.; Komeiji, Y.
Source: Self-asserted source
Yuto Komeiji via Scopus - Elsevier

Accuracy of the fragment molecular orbital (FMO) calculations for DNA: Total energy, molecular orbital, and inter-fragment interaction energy

Computational and Theoretical Chemistry
2014 | Journal article
DOI: 10.1016/j.comptc.2014.02.002
EID:

2-s2.0-84897591358
Contributors: Fukuzawa, K.; Watanabe, C.; Kurisaki, I.; Taguchi, N.; Mochizuki, Y.; Nakano, T.; Tanaka, S.; Komeiji, Y.
Source: Self-asserted source
Yuto Komeiji via Scopus - Elsevier

Electron-correlated fragment-molecular-orbital calculations for biomolecular and nano systems

Physical Chemistry Chemical Physics
2014 | Journal article
DOI: 10.1039/c4cp00316k
EID:

2-s2.0-84900816215
Contributors: Tanaka, S.; Mochizuki, Y.; Komeiji, Y.; Okiyama, Y.; Fukuzawa, K.
Source: Self-asserted source
Yuto Komeiji via Scopus - Elsevier

Fragment molecular orbital-based molecular dynamics (FMO-MD) simulations on hydrated Cu(II) ion

Chem-Bio Informatics Journal
2014 | Journal article
DOI: 10.1273/cbij.14.1
EID:

2-s2.0-84903780656
Contributors: Kato, Y.; Fujiwara, T.; Komeiji, Y.; Nakano, T.; Mori, H.; Okiyama, Y.; Mochizuki, Y.
Source: Self-asserted source
Yuto Komeiji via Scopus - Elsevier

Differences in hydration between cis- and trans-platin: Quantum insights by ab initio fragment molecular orbital-based molecular dynamics (FMO-MD)

Computational and Theoretical Chemistry
2012 | Journal article
DOI: 10.1016/j.comptc.2012.02.008
EID:

2-s2.0-84858864350
Contributors: Mori, H.; Hirayama, N.; Komeiji, Y.; Mochizuki, Y.
Source: Self-asserted source
Yuto Komeiji via Scopus - Elsevier

FMO-MD simulations on the hydration of formaldehyde in water solution with constraint dynamics

Chemistry - A European Journal
2012 | Journal article
DOI: 10.1002/chem.201200874
EID:

2-s2.0-84864117122
Contributors: Sato, M.; Yamataka, H.; Komeiji, Y.; Mochizuki, Y.
Source: Self-asserted source
Yuto Komeiji via Scopus - Elsevier

Fragment molecular orbital-based molecular dynamics (FMO-MD) method with MP2 gradient

Chemical Physics Letters
2011 | Journal article
DOI: 10.1016/j.cplett.2011.01.039
EID:

2-s2.0-79952009636
Contributors: Mochizuki, Y.; Nakano, T.; Komeiji, Y.; Yamashita, K.; Okiyama, Y.; Yoshikawa, H.; Yamataka, H.
Source: Self-asserted source
Yuto Komeiji via Scopus - Elsevier

Does amination of formaldehyde proceed through a zwitterionic intermediate in water? Fragment molecular orbital molecular dynamics simulations by using constraint dynamics

Chemistry - A European Journal
2010 | Journal article
DOI: 10.1002/chem.201000442
EID:

2-s2.0-77953142537
Contributors: Sato, M.; Yamataka, H.; Komeiji, Y.; Mochizuki, Y.; Nakano, T.
Source: Self-asserted source
Yuto Komeiji via Scopus - Elsevier

Fragment molecular orbital-based molecular dynamics (FMO-MD) simulations on hydrated Zn(II) ion

Chemical Physics Letters
2010 | Journal article
DOI: 10.1016/j.cplett.2010.03.020
EID:

2-s2.0-77950296945
Contributors: Fujiwara, T.; Mochizuki, Y.; Komeiji, Y.; Okiyama, Y.; Mori, H.; Nakano, T.; Miyoshi, E.
Source: Self-asserted source
Yuto Komeiji via Scopus - Elsevier

Three-body expansion and generalized dynamic fragmentation improve the fragment molecular orbital-based molecular dynamics (FMO-MD)

Chemical Physics Letters
2010 | Journal article
DOI: 10.1016/j.cplett.2009.11.045
EID:

2-s2.0-72649103822
Contributors: Komeiji, Y.; Mochizuki, Y.; Nakano, T.
Source: Self-asserted source
Yuto Komeiji via Scopus - Elsevier

Fragment molecular orbital method-based molecular dynamics (FMO-MD) as a simulator for chemical reactions in explicit solvation

Journal of Computational Chemistry
2009 | Journal article
DOI: 10.1002/jcc.21025
EID:

2-s2.0-58149241004
Contributors: Komeiji, Y.; Ishikawa, T.; Mochizuki, Y.; Yamataka, H.; Nakano, T.
Source: Self-asserted source
Yuto Komeiji via Scopus - Elsevier

Fragment molecular orbital-based molecular dynamics (FMO-MD), a quantum simulation tool for large molecular systems

Journal of Molecular Structure: THEOCHEM
2009 | Journal article
DOI: 10.1016/j.theochem.2008.07.001
EID:

2-s2.0-60749099088
Contributors: Komeiji, Y.; Mochizuki, Y.; Nakano, T.; Fedorov, D.G.
Source: Self-asserted source
Yuto Komeiji via Scopus - Elsevier

How does an S<inf>N</inf>2 reaction take place in solution? Full Ab iInitio MD simulations for the hydrolysis of the methyl diazonium ion

Journal of the American Chemical Society
2008 | Journal article
DOI: 10.1021/ja710038c
EID:

2-s2.0-39749109342
Contributors: Sato, M.; Yamataka, H.; Komeiji, Y.; Mochizuki, Y.; Ishikawa, T.; Nakano, T.
Source: Self-asserted source
Yuto Komeiji via Scopus - Elsevier

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
2008 | Journal article
DOI: 10.1016/j.compbiolchem.2008.01.001
EID:

2-s2.0-43249090774
Contributors: VanSchouwen, B.M.B.; Gordon, H.L.; Rothstein, S.M.; Komeiji, Y.; Fukuzawa, K.; Tanaka, S.
Source: Self-asserted source
Yuto Komeiji via Scopus - Elsevier

A fully quantum mechanical simulation study on the lowest n-Ï€<sup>*</sup> state of hydrated formaldehyde

Chemical Physics Letters
2007 | Journal article
DOI: 10.1016/j.cplett.2007.02.016
EID:

2-s2.0-33847253334
Contributors: Mochizuki, Y.; Komeiji, Y.; Ishikawa, T.; Nakano, T.; Yamataka, H.
Source: Self-asserted source
Yuto Komeiji via Scopus - Elsevier

Ab initio FMO-MD method reimplemented and applied to pure water

AIP Conference Proceedings
2007 | Conference paper
DOI: 10.1063/1.2835978
EID:

2-s2.0-71449114464
Contributors: Komeiji, Y.; Ishikawa, T.; Mochizuki, Y.; Yamataka, H.; Nakano, T.
Source: Self-asserted source
Yuto Komeiji via Scopus - Elsevier

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
2007 | Journal article
DOI: 10.1002/jcc.20686
EID:

2-s2.0-34547317046
Contributors: Komeiji, Y.; Ishida, T.; Fedorov, D.G.; Kitaura, K.
Source: Self-asserted source
Yuto Komeiji via Scopus - Elsevier

Erratum: Intra- and intermodular interactions between cyclic-AMP receptor protein and DNA: Ab initio fragment molecular orbital study (Journal of Computational Chemistry (2006) 27 (948))

Journal of Computational Chemistry
2007 | Journal article
DOI: 10.1002/jcc.20803
EID:

2-s2.0-34547927753
Contributors: Fukuzawa, K.; Komeiji, Y.; Mochizuki, Y.; Kato, A.; Nakano, T.; Tanaka, S.
Source: Self-asserted source
Yuto Komeiji via Scopus - Elsevier

Implementation of the blue moon ensemble method

Chem-Bio Informatics Journal
2007 | Journal article
DOI: 10.1273/cbij.7.12
EID:

2-s2.0-39149132143
Contributors: Komeiji, Y.
Source: Self-asserted source
Yuto Komeiji via Scopus - Elsevier

Visualization analysis of inter-fragment interaction energies of CRP-cAMP-DNA complex based on the fragment molecular orbital method

Biophysical Chemistry
2007 | Journal article
DOI: 10.1016/j.bpc.2007.06.011
EID:

2-s2.0-34548779129
Contributors: Kurisaki, I.; Fukuzawa, K.; Komeiji, Y.; Mochizuki, Y.; Nakano, T.; Imada, J.; Chmielewski, A.; Rothstein, S.M.; Watanabe, H.; Tanaka, S.
Source: Self-asserted source
Yuto Komeiji via Scopus - Elsevier

Fragment molecular orbital calculations on large scale systems containing heavy metal atom

Chemical Physics Letters
2006 | Journal article
DOI: 10.1016/j.cplett.2006.06.103
EID:

2-s2.0-33746356567
Contributors: Ishikawa, T.; Mochizuki, Y.; Nakano, T.; Amari, S.; Mori, H.; Honda, H.; Fujita, T.; Tokiwa, H.; Tanaka, S.; Komeiji, Y. et al.
Source: Self-asserted source
Yuto Komeiji via Scopus - Elsevier

Intra- and intermolecular interactions between cyclic-AMP receptor protein and DNA: Ab initio fragment molecular orbital study

Journal of Computational Chemistry
2006 | Journal article
DOI: 10.1002/jcc.20399
EID:

2-s2.0-33646586407
Contributors: Fukuzawa, K.; Komeiji, Y.; Mochizuki, Y.; Kato, A.; Nakano, T.; Tanaka, S.
Source: Self-asserted source
Yuto Komeiji via Scopus - Elsevier

Ab initio fragment molecular orbital (FMO) method applied to analysis of the ligand-protein interaction in a pheromone-binding protein

Computational Biology and Chemistry
2005 | Journal article
DOI: 10.1016/j.compbiolchem.2005.09.005
EID:

2-s2.0-28044438176
Contributors: Nemoto, T.; Fedorov, D.G.; Uebayasi, M.; Kanazawa, K.; Kitaura, K.; Komeiji, Y.
Source: Self-asserted source
Yuto Komeiji via Scopus - Elsevier

PEACH 4 with ABINIT-MP: A general platform for classical and quantum simulations of biological molecules

Computational Biology and Chemistry
2004 | Journal article
DOI: 10.1016/j.compbiolchem.2004.01.003
EID:

2-s2.0-2342473845
Contributors: Komeiji, Y.; Inadomi, Y.; Nakano, T.
Source: Self-asserted source
Yuto Komeiji via Scopus - Elsevier

Fragment molecular orbital method: Application to molecular dynamics simulation, 'ab initio FMO-MD'

Chemical Physics Letters
2003 | Journal article
DOI: 10.1016/S0009-2614(03)00430-5
EID:

2-s2.0-0344950464
Contributors: Komeiji, Y.; Nakano, T.; Fukuzawa, K.; Ueno, Y.; Inadomi, Y.; Nemoto, T.; Uebayasi, M.; Fedorov, D.G.; Kitaura, K.
Source: Self-asserted source
Yuto Komeiji via Scopus - Elsevier

Erratum: Molecular dynamics simulations revealed Ca2+-dependent conformational change of Calmodulin (FEBS Letters (2002) 521 (133-139) PII: S0014579302028533)

FEBS Letters
2002 | Journal article
DOI: 10.1016/S0014-5793(02)02989-7
EID:

2-s2.0-0037125189
Contributors: Komeiji, Y.; Ueno, Y.; Uebayasi, M.
Source: Self-asserted source
Yuto Komeiji via Scopus - Elsevier

Flexibility of a loop in a pheromone binding protein from Bombyx mori: A molecular dynamics simulation

Chem-Bio Informatics Journal
2002 | Journal article
DOI: 10.1273/cbij.2.32
EID:

2-s2.0-28044470138
Contributors: Nemoto, T.; Uebayasi, M.; Komeiji, Y.
Source: Self-asserted source
Yuto Komeiji via Scopus - Elsevier

Molecular dynamics simulations revealed Ca<sup>2+</sup>-dependent conformational change of Calmodulin

FEBS Letters
2002 | Journal article
DOI: 10.1016/S0014-5793(02)02853-3
EID:

2-s2.0-0037134854
Contributors: Komeiji, Y.; Ueno, Y.; Uebayasi, M.
Source: Self-asserted source
Yuto Komeiji via Scopus - Elsevier

Peach-Grape system - A high performance simulator for biomolecules

Chem-Bio Informatics Journal
2002 | Journal article
DOI: 10.1273/cbij.2.102
EID:

2-s2.0-33646120268
Contributors: Komeiji, Y.; Uebayasi, M.
Source: Self-asserted source
Yuto Komeiji via Scopus - Elsevier
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