創薬基盤としての分子動力学シミュレーション技術
藤谷秀章(東京大学　先端科学技術研究センター)
学術の動向,22巻(2017) 7号 p. 7_58-7_61, DOI:10.5363/tits.22.7_58

Multiscale Molecular Dynamics Simulations of Rotary Motor Proteins
Toru Ekimoto(Yokohama City University), Mitsunori Ikeguchi(Yokohama City University)
Biophys. Rev.,10, 605-615, DOI:10.1007/s12551-017-0373-4

Toward rational antibody design: recent advancements in molecular dynamics simulations
Takefumi Yamashita(the University of Tokyo)
Int. Immunol.,30, 133－140 (2018), DOI:10.1093/intimm/dxx077

Free energy profiles for unwrapping the outer superhelical turn of nucleosomal DNA
Hidetoshi Kono(QST), Shun Sakuraba(Univ. of Tokyo), Hisashi Ishida(QST)
PLOS Computational Biology,Vol.14, pp.e1006024 (2018), DOI:10.1371/journal.pcbi.1006024

Identification of Factors Promoting HBV Capsid Self-Assembly by Assembly-Promoting Antivirals
Soumya Lipsa Rath(Nagoya University, Department of Materials Chemistry), Huihui Liu(Nagoya University, Department of Materials Chemistry), Susumu Okazaki(Nagoya University, Department of Materials Chemistry), Wataru shinoda(Nagoya University, Department of Materials Chemistry)
J. Chem. Info. Mod,vol.58. 328-337, DOI:10.1021/acs.jcim.7b00471

Initiation of prolyl cis-trans isomerisation in the CDR-H3 loop of an antibody in response to antigen binding
Keiko Shinoda(RCAST, The University of Tokyo), Hideaki Fujitani(RCAST, The University of Tokyo)
Scientific Reports, 7(1):16964 (2017), DOI:10.1038/s41598-017-16766-8

An Ensemble Docking Calculation of Lysozyme and HyHEL-10: Insight into the Binding Mechanism
Takefumi Yamashita, Yuichiro Takamatsu(the University of Tokyo)
AIP Conference Proceedings,1906, 030022 (2017), DOI:10.1063/1.5012301

Accessibility of the histone H3 tail in the nucleosome for binding of paired readers
Jovylyn Gatchalian(Department of Pharmacology, University of Colorado School of Medicine, Aurora, CO 80045, USA.), Xiaodong Wang(Department of Biochemistry and Biophysics, University of Rochester Medical Center, Rochester, NY 14642, USA.), Jinzen Ikebe(Molecular Modeling and Simulation Group, National Institutes for Quantum and Radiological Science and Technology, Kizugawa, Kyoto, 619 0215, Japan.), Khan L. Cox(Department of Physics, Ohio State University, Columbus, OH, 43210, USA.), Adam H. Tencer(Department of Pharmacology, University of Colorado School of Medicine, Aurora, CO 80045, USA.), Yi Zhang(Department of Pharmacology, University of Colorado School of Medicine, Aurora, CO 80045, USA.), Nathaniel L. Burge(Department of Physics, Ohio State University, Columbus, OH, 43210, USA.), Luo Di(Molecular Modeling and Simulation Group, National Institutes for Quantum and Radiological Science and Technology, Kizugawa, Kyoto, 619 0215, Japan.), Matthew D. Gibson(Department of Physics, Ohio State University, Columbus, OH, 43210, USA.), Catherine A. Musselman(Department of Biochemistry, University of Iowa College of Medicine, Iowa City, IA 52242, USA.), Michael G. Poirier(Department of Physics, Ohio State University, Columbus, OH, 43210, USA.), Hidetoshi Kono(Molecular Modeling and Simulation Group, National Institutes for Quantum and Radiological Science and Technology, Kizugawa, Kyoto, 619 0215, Japan.), Jeffrey J. Hayes(Department of Biochemistry and Biophysics, University of Rochester Medical Center, Rochester, NY 14642, USA.), Tatiana G. Kutateladze(Department of Pharmacology, University of Colorado School of Medicine, Aurora, CO 80045, USA.)
Nature Communications,Vol.8, 1489(2017), DOI:10.1038/s41467-017-01598-x

Covalent modifications of histone H3K9 promote binding of CHD3
Adam H. Tencer(Department of Pharmacology, University of Colorado School of Medicine), Khan L. Cox(Department of Physics, Ohio State University), Luo Di(Molecular Modeling and Simulation Group, Natinal Institutes for Quantum and Radiological Science and Technology), Joseph B. Bridgers(Department of Biochemistry and Biophysics and the Lineberger Comprehensive Cancer Center, University of North Carolina School of Medicine), Jie Lyu(Dan L. Duncan Cancer Center, Department of Molecular and Cellular Biology, Baylor College of Medicine), Xiaodong Wang(Department of Biochemistry and Biophysics, University of Rochester Medical Center), Jennifer K. Sims(Laboratory of Molecular Carcinogenesis, National Institute of Environmental Health Sciences), Tyler M. Weaver(Department of Biochemistry, University of lowa College of Medicine), Hillary F. Allen(Department of Pharmacology, University of Colorado School of Medicine), Yi Zhang(Department of Pharmacology, University of Colorado School of Medicine), Jovylyn Gatchalian(Department of Pharmacology, University of Colorado School of Medicine), Michael A. Darcy(Department of Physics, Ohio State University), Matthew D. Gibson(Department of Physics, Ohio State University), Jinzen Ikebe(Molecular Modeling and Simulation Group, Natinal Institutes for Quantum and Radiological Science and Technology), Wei Li(Dan L. Duncan Cancer Center, Department of Molecular and Cellular Biology, Baylor College of Medicine), Paul A. Wade(Laboratory of Molecular Carcinogenesis, National Institute of Environmental Health Sciences), Jeffrey J. Hayes(Department of Biochemistry and Biophysics, University of Rochester Medical Center), Brian D. Strahl(Department of Biochemistry and Biophysics and the Lineberger Comprehensive Cancer Center, University of North Carolina School of Medicine), Hidetoshi Kono(Molecular Modeling and Simulation Group, Natinal Institutes for Quantum and Radiological Science and Technology), Michael G. Poirier(Department of Physics, Ohio State University), Catherine A. Musselman(Department of Biochemistry, University of lowa College of Medicine), Tatiana G. Kutateladze(Department of Pharmacology, University of Colorado School of Medicine)
Cell Reports,Vol.21, pp.455-466 (2017), DOI:10.1016/j.celrep.2017.09.054

H4 Tails Potentially Produce the Diversity in the Orientation of Two Nucleosomes
Ishida, Hisashi; Kono, Hidetoshi(Molecular Modeling and Simulation Group, Quantum Beam Science Research Directorate, National Institutes fo Quantum and RadiologicalScience and Technology)
BIOPHYSICAL JOURNAL,Vol.113-5 (2017), pp.978-990, DOI:10.1016/j.bpj.2017.07.015

Rotation Mechanism of Molecular Motor V-1-ATPase Studied by Multiscale Molecular Dynamics Simulation
Yuta Isaka(Yokohama City University), Toru Ekimoto(Yokohama City University), Yuichi Kokabu(Yokohama City University), Ichiro Yamato(Tokyo University of Science), Takeshi Murata(Chiba University), Mitsunori Ikeguchi(Yokohama City University)
Biophysical Journal,112, 911-920, DOI:10.1016/j.bpj.2017.01.029

高速分子動力学シミュレーションと創薬
藤谷　秀章(東京大学　先端科学技術研究センター)
日本シミュレーション学会誌　「シミュレーション」, Vol.36 No.3 pp16-21

創薬基盤としての分子動力学シミュレーション技術
藤谷秀章(東京大学　先端科学技術研究センター)
学術の動向, 22巻(2017) 7号 p. 7_58-7_61, DOI:10.5363/tits.22.7_58

京速コンピューティングによる創薬への挑戦: ポスト「京」時代に向けて
山下雄史(東京大学)
分子シミュレーション研究会会誌「アンサンブル」, 19(2) 81-87 (2017), DOI:10.11436/mssj.19.81

ヌクレオソーム中におけるH3ヒストンテールの構造とアセチル化の影響
池部仁善(量研機構), 櫻庭俊(東大), 河野秀俊(量研機構)
日本生物物理学会誌, 生物物理 57 (2)，095-097( 2017), DOI:10.2142/biophys.57.095

Computational Methods for Configurational Entropy Using Internal and Cartesian Coordinates.
Hikiri S, Yoshidome T, Ikeguchi M(Yokohama City University)
J Chem Theory Comput, 12, 5990-6000(2016), DOI:10.1021/acs.jctc.6b00563

Towards Physical Understanding of Molecular Recognition in the Cell: Recent Evolution of Molecular Dynamics Techniques and Free Energy Theories
Takefumi Yamashita(Univ. Tokyo)
Biomedical Sciences,2(5): 34-47(2016), DOI:10.11648/j.bs.20160205.11

Apo- and Antagonist-Binding Structures of Vitamin D Receptor Ligand-Binding Domain Revealed by Hybrid Approach Combining Small-Angle X-ray Scattering and Molecular Dynamics.
Anami Y, Egawa D, Itoh T, Yamamoto K(Showa Pharmaceutical University), Shimizu N(Photon Factory, Institute of Materials Structure Science, High Energy Accelerator Research Organization (KEK)), Ekimoto T, Ikeguchi M(Yokohama City University)
J Med Chem., 59, 7888-900.(2016), DOI:10.1021/acs.jmedchem.6b00682

Coarse-Grained Molecular Dynamics Study of Membrane Fusion: Curvature Effects on Free Energy Barrieres along the Stalk Mechanism
Shuhei Kawamoto(Nagoya University), Michael L. Klein(Temple University), Wataru Shinoda(Nagoya University)
The Journal of Chemical Physics,Vol. 143, 243112 (2015), DOI:http://dx.doi.org/10.1063/1.4933087