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Protein Data Bank Japan: Improved tools for sequence‐oriented analysis of protein structures
Gert‐Jan Bekker, Chioko Nagao, Matsuyuki Shirota, Tsukasa Nakamura, Toshiaki Katayama, Daisuke Kihara, Kengo Kinoshita, Genji Kurisu
Protein Science 2025/03 Research paper (scientific journal)
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Protein Data Bank Japan: Computational resources for analysis of protein structures
Gert-Jan Bekker, Chioko Nagao, Matsuyuki Shirota, Tsukasa Nakamura, Toshiaki Katayama, Daisuke Kihara, Kengo Kinoshita, Genji Kurisu
Journal of Molecular Biology 2025/02 Research paper (scientific journal)
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Structural dynamics of the Ca2+-regulated cutinase towards structure-based improvement of PET degradation activity
Nobutaka Numoto, Fumiya Kondo, Gert-Jan Bekker, Zengwei Liao, Mitsuaki Yamashita, Akira Iida, Nobutoshi Ito, Narutoshi Kamiya, Masayuki Oda
International Journal of Biological Macromolecules Vol. 281 p. 136597-136597 2024/11 Research paper (scientific journal)
Publisher: Elsevier BV
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Molecular Dynamics Unveils Multiple-Site Binding of Inhibitors with Reduced Activity on the Surface of Dihydrofolate Reductase
Mitsugu Araki, Toru Ekimoto, Kazuhiro Takemura, Shigeyuki Matsumoto, Yunoshin Tamura, Hironori Kokubo, Gert-Jan Bekker, Tsutomu Yamane, Yuta Isaka, Yukari Sagae, Narutoshi Kamiya, Mitsunori Ikeguchi, Yasushi Okuno
Journal of the American Chemical Society 2024/10/12 Research paper (scientific journal)
Publisher: American Chemical Society (ACS)
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Familial Episodic Pain Syndrome: A Japanese Family Harboring the Novel Variant c.2431C>T (p.Leu811Phe) in SCN11A
Chioko Nagao, Hiroko Okuda, Gert-Jan Bekker, Atsuko Noguchi, Tsutomu Takahashi, Akio Koizumi, Shohab Youssefian, Tohru Tezuka, Shinji Akioka
Biochemical Genetics 2024/07/25 Research paper (scientific journal)
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Binding Mechanism between Platelet Glycoprotein and Cyclic Peptide Elucidated by McMD-Based Dynamic Docking
Gert-Jan Bekker, Kanji Oshima, Mitsugu Araki, Yasushi Okuno, Narutoshi Kamiya
Journal of Chemical Information and Modeling Vol. 64 No. 10 p. 4158-4167 2024/05/16 Research paper (scientific journal)
Publisher: American Chemical Society (ACS)
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Binding Mechanism of Riboswitch to Natural Ligand Elucidated by McMD-Based Dynamic Docking Simulations
Gert-Jan Bekker, Yoshifumi Fukunishi, Junichi Higo, Narutoshi Kamiya
ACS Omega 2024/01/10 Research paper (scientific journal)
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Enhanced Coarse-Grained Molecular Dynamics Simulation with a Smoothed Hybrid Potential Using a Neural Network Model
Ryo Kanada, Atsushi Tokuhisa, Yusuke Nagasaka, Shingo Okuno, Koichiro Amemiya, Shuntaro Chiba, Gert-Jan Bekker, Narutoshi Kamiya, Koichiro Kato, Yasushi Okuno
Journal of Chemical Theory and Computation 2024/01/09 Research paper (scientific journal)
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Elucidation of binding mechanism, affinity and complex structure between mWT1 tumor‐associated antigen peptide and HLA‐A*24:02
Gert‐Jan Bekker, Nobutaka Numoto, Maki Kawasaki, Takahiro Hayashi, Saaya Yabuno, Yuko Kozono, Takeyuki Shimizu, Haruo Kozono, Nobutoshi Ito, Masayuki Oda, Narutoshi Kamiya
Protein Science 2023/09/04 Research paper (scientific journal)
Publisher: Wiley
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Mutual induced-fit mechanism drives binding between intrinsically disordered Bim and cryptic binding site of Bcl-xL
Gert-Jan Bekker, Mitsugu Araki, Kanji Oshima, Yasushi Okuno, Narutoshi Kamiya
Communications Biology Vol. 6 No. 1 2023/03/30 Research paper (scientific journal)
Publisher: Springer Science and Business Media LLC
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Binding free-energy landscapes of small molecule binder and non-binder to FMN riboswitch: All-atom molecular dynamics
Junichi Higo, Gert-Jan Bekker, Narutoshi Kamiya, Ikuo Fukuda, Yoshifumi Fukunishi
Biophysics and Physicobiology 2023 Research paper (scientific journal)
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Thermal Stability Estimation of Single Domain Antibodies Using Molecular Dynamics Simulations
Gert-Jan Bekker, Narutoshi Kamiya
Computer-Aided Antibody Design p. 151-163 2023 Part of collection (book)
Publisher: Springer US
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History of Protein Data Bank Japan: standing at the beginning of the age of structural genomics
Genji Kurisu, Gert-Jan Bekker, Atsushi Nakagawa
Biophysical Reviews 2022/12/09 Research paper (scientific journal)
Publisher: Springer Science and Business Media LLC
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Advancing the field of computational drug design using multicanonical molecular dynamics-based dynamic docking
Gert-Jan Bekker, Narutoshi Kamiya
Biophysical Reviews Vol. 14 No. 6 p. 1349-1358 2022/11/19 Research paper (scientific journal)
Publisher: Springer Science and Business Media LLC
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Fly casting with ligand sliding and orientational selection supporting complex formation of a GPCR and a middle sized flexible molecule
Junichi Higo, Kota Kasahara, Gert-Jan Bekker, Benson Ma, Shun Sakuraba, Shinji Iida, Narutoshi Kamiya, Ikuo Fukuda, Hidetoshi Kono, Yoshifumi Fukunishi, Haruki Nakamura
Scientific Reports Vol. 12 No. 1 2022/08/13 Research paper (scientific journal)
Publisher: Springer Science and Business Media LLC
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Protein Data Bank Japan: Celebrating our 20th anniversary during a global pandemic as the Asian hub of three dimensional macromolecular structural data.
Gert-Jan Bekker, Masashi Yokochi, Hirofumi Suzuki, Yasuyo Ikegawa, Takeshi Iwata, Takahiro Kudou, Kei Yura, Toshimichi Fujiwara, Takeshi Kawabata, Genji Kurisu
Protein science : a publication of the Protein Society Vol. 31 No. 1 p. 173-186 2022/01 Research paper (scientific journal)
Publisher: Wiley
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N-Terminal-Driven Binding Mechanism of an Antigen Peptide to Human Leukocyte Antigen-A*2402 Elucidated by Multicanonical Molecular Dynamic-Based Dynamic Docking and Path Sampling Simulations
Gert-Jan Bekker, Narutoshi Kamiya
The Journal of Physical Chemistry B 2021/12/03 Research paper (scientific journal)
Publisher: American Chemical Society (ACS)
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Exploring ligand binding pathways on proteins using hypersound-accelerated molecular dynamics
Mitsugu Araki, Shigeyuki Matsumoto, Gert-Jan Bekker, Yuta Isaka, Yukari Sagae, Narutoshi Kamiya, Yasushi Okuno
Nature Communications Vol. 12 No. 1 2021/12 Research paper (scientific journal)
Publisher: Springer Science and Business Media LLC
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Cryptic-site binding mechanism of medium-sized Bcl-xL inhibiting compounds elucidated by McMD-based dynamic docking simulations
Gert-Jan Bekker, Ikuo Fukuda, Junichi Higo, Yoshifumi Fukunishi, Narutoshi Kamiya
Scientific Reports Vol. 11 No. 1 2021/12 Research paper (scientific journal)
Publisher: Springer Science and Business Media LLC
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Accurate Binding Configuration Prediction of a G-Protein-Coupled Receptor to Its Antagonist Using Multicanonical Molecular Dynamics-Based Dynamic Docking
Gert-Jan Bekker, Mitsugu Araki, Kanji Oshima, Yasushi Okuno, Narutoshi Kamiya
Journal of Chemical Information and Modeling Vol. 61 No. 10 p. 5161-5171 2021/10/25 Research paper (scientific journal)
Publisher: American Chemical Society ({ACS})
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Structural basis of mutants of PET-degrading enzyme from Saccharomonospora viridis AHK190 with high activity and thermal stability.
Miho Emori, Nobutaka Numoto, Akane Senga, Gert-Jan Bekker, Narutoshi Kamiya, Yuma Kobayashi, Nobutoshi Ito, Fusako Kawai, Masayuki Oda
Proteins Vol. 89 No. 5 p. 502-511 2021/05 Research paper (scientific journal)
Publisher: Wiley
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Dynamical Methods to Study Interaction in Proteins Facilitating Molecular Understanding of Cancer
Bhaskar Dasgupta, Gert-Jan Bekker, Narutoshi Kamiya
Handbook of Oxidative Stress in Cancer: Mechanistic Aspects p. 1-17 2021
Publisher: Springer Singapore
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Dynamic Docking Using Multicanonical Molecular Dynamics: Simulating Complex Formation at the Atomistic Level
Gert-Jan Bekker, Narutoshi Kamiya
Methods in Molecular Biology p. 187-202 2021 Part of collection (book)
Publisher: Springer US
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Cutinases from thermophilic bacteria (actinomycetes): From identification to functional and structural characterization
Masayuki Oda, Nobutaka Numoto, Gert-Jan Bekker, Narutoshi Kamiya, Fusako Kawai
Methods in Enzymology p. 159-185 2021 Part of collection (book)
Publisher: Elsevier
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Exhaustive search of the configurational space of heat‐shock protein 90 with its inhibitor by multicanonical molecular dynamics based dynamic docking
Gert‐Jan Bekker, Mitsugu Araki, Kanji Oshima, Yasushi Okuno, Narutoshi Kamiya
Journal of Computational Chemistry Vol. 41 No. 17 p. 1606-1615 2020/06/30 Research paper (scientific journal)
Publisher: Wiley
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The Biological Structure Model Archive (BSM-Arc): an archive for in silico models and simulations
Gert-Jan Bekker, Takeshi Kawabata, Genji Kurisu
Biophysical Reviews Vol. 12 No. 2 p. 371-375 2020/04/05 Research paper (scientific journal)
Publisher: Springer Science and Business Media {LLC}
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Mutual population-shift driven antibody-peptide binding elucidated by molecular dynamics simulations
Gert-Jan Bekker, Ikuo Fukuda, Junichi Higo, Narutoshi Kamiya
Scientific Reports Vol. 10 No. 1 2020/01/29 Research paper (scientific journal)
Publisher: Springer Science and Business Media {LLC}
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PDBx/mmCIF Format Mandatory for Protein Data Bank Deposition
Gert-Jan Bekker
Nihon Kessho Gakkaishi Vol. 61 No. 3 p. 159-160 2019/08/31 Research paper (scientific journal)
Publisher: The Crystallographic Society of Japan
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Dynamic Docking of a Medium-Sized Molecule to Its Receptor by Multicanonical MD Simulations
Gert-Jan Bekker, Mitsugu Araki, Kanji Oshima, Yasushi Okuno, Narutoshi Kamiya
The Journal of Physical Chemistry B 2019/03/21 Research paper (scientific journal)
Publisher: American Chemical Society ({ACS})
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Metal binding to cutinase-like enzyme from Saccharomonospora viridis AHK190 and its effects on enzyme activity and stability
Akane Senga, Yoshiji Hantani, Gert-Jan Bekker, Narutoshi Kamiya, Yuki Kimura, Fusako Kawai, Masayuki Oda
The Journal of Biochemistry 2019/03/02 Research paper (scientific journal)
Publisher: Oxford University Press ({OUP})
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Protein Data Bank: the single global archive for 3D macromolecular structure data
wwPDB consortium
Nucleic Acids Research Vol. 47 No. D1 p. D520-D528 2018/10 Research paper (scientific journal)
Publisher: Oxford University Press ({OUP})
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Structural Dynamics of the PET-Degrading Cutinase-like Enzyme from Saccharomonospora viridis AHK190 in Substrate-Bound States Elucidates the Ca2+-Driven Catalytic Cycle
Nobutaka Numoto, Narutoshi Kamiya, Gert-Jan Bekker, Yuri Yamagami, Satomi Inaba, Kentaro Ishii, Susumu Uchiyama, Fusako Kawai, Nobutoshi Ito, Masayuki Oda
Biochemistry Vol. 57 No. 36 p. 5289-5300 2018/09/11 Research paper (scientific journal)
Publisher: American Chemical Society ({ACS})
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Folding thermodynamics of PET-hydrolyzing enzyme Cut190 depending on Ca2+ concentration
Satomi Inaba, Narutoshi Kamiya, Gert-Jan Bekker, Fusako Kawai, Masayuki Oda
Journal of Thermal Analysis and Calorimetry Vol. 135 No. 5 p. 2655-2663 2018/06/04 Research paper (scientific journal)
Publisher: Springer Nature
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Structural and thermodynamic characterization of endo-1,3-β-glucanase: Insights into the substrate recognition mechanism
Masayuki Oda, Satomi Inaba, Narutoshi Kamiya, Gert-Jan Bekker, Bunzo Mikami
Biochimica et Biophysica Acta (BBA) - Proteins and Proteomics Vol. 1866 No. 3 p. 415-425 2018/03 Research paper (scientific journal)
Publisher: Elsevier {BV}
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Thermal stability of single-domain antibodies estimated by molecular dynamics simulations
Gert-Jan Bekker, Benson Ma, Narutoshi Kamiya
Protein Science Vol. 28 No. 2 p. 429-438 2018 Research paper (scientific journal)
Publisher: Wiley
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New tools and functions in data-out activities at Protein Data Bank Japan (PDBj)
Akira R. Kinjo, Gert-Jan Bekker, Hiroshi Wako, Shigeru Endo, Yuko Tsuchiya, Hiromu Sato, Hafumi Nishi, Kengo Kinoshita, Hirofumi Suzuki, Takeshi Kawabata, Masashi Yokochi, Takeshi Iwata, Naohiro Kobayashi, Toshimichi Fujiwara, Genji Kurisu, Haruki Nakamura
Protein Science Vol. 27 No. 1 p. 95-102 2017/09 Research paper (scientific journal)
Publisher: Wiley
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Accurate Prediction of Complex Structure and Affinity for a Flexible Protein Receptor and Its Inhibitor
Gert-Jan Bekker, Narutoshi Kamiya, Mitsugu Araki, Ikuo Fukuda, Yasushi Okuno, Haruki Nakamura
Journal of Chemical Theory and Computation Vol. 13 No. 6 p. 2389-2399 2017/05 Research paper (scientific journal)
Publisher: American Chemical Society ({ACS})
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Protein Data Bank Japan (PDBj): updated user interfaces, resource description framework, analysis tools for large structures
Akira R. Kinjo, Gert-Jan Bekker, Hirofumi Suzuki, Yuko Tsuchiya, Takeshi Kawabata, Yasuyo Ikegawa, Haruki Nakamura
Nucleic Acids Research Vol. 45 No. D1 p. D282-D288 2016/10 Research paper (scientific journal)
Publisher: Oxford University Press ({OUP})
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Molmil: a molecular viewer for the PDB and beyond
Gert-Jan Bekker, Haruki Nakamura, Akira R. Kinjo
Journal of Cheminformatics Vol. 8 No. 1 2016/08 Research paper (scientific journal)
Publisher: Springer Nature