Gert-Jan Bekker

ORCID

Publication Activity (10 Years)

Years Active: 2018-2024
Publications (10 Years): 21

Top Venues

Journal of chemical information and modeling

Communications biology

Biophysical reviews

The journal of physical chemistry. B

Osaka Daigaku

Osaka Daigaku (PHD)

This page only lists publications with an associated author ORCID identifier.

Affiliation History

Osaka Daigaku

Japan

Specially Appointed Assistant Professor

Osaka Daigaku

Japan

Researcher

Education History

Osaka Daigaku

Japan

PHD

Radboud Universiteit Nijmegen Faculteit der Natuurwetenschappen Wiskunde en Informatica

Netherlands

MSC

Publications

Gert-Jan Bekker, Kanji Oshima, Mitsugu Araki, Yasushi Okuno, Narutoshi Kamiya
Binding Mechanism between Platelet Glycoprotein and Cyclic Peptide Elucidated by McMD-Based Dynamic Docking. Journal of chemical information and modeling 64 (10) (2024)
Gert-Jan Bekker, Yoshifumi Fukunishi, Junichi Higo, Narutoshi Kamiya
Binding Mechanism of Riboswitch to Natural Ligand Elucidated by McMD-Based Dynamic Docking Simulations. ACS omega 9 (3) (2024)
Gert-Jan Bekker, Kanji Oshima, Mitsugu Araki, Yasushi Okuno, Narutoshi Kamiya
Binding Mechanism between Platelet Glycoprotein and Cyclic Peptide Elucidated by McMD-Based Dynamic Docking. Journal of chemical information and modeling (2024)
Gert-Jan Bekker, Yoshifumi Fukunishi, Junichi Higo, Narutoshi Kamiya
Binding Mechanism of Riboswitch to Natural Ligand Elucidated by McMD-Based Dynamic Docking Simulations. ACS omega 9 (3) (2024)
Gert-Jan Bekker, Kanji Oshima, Mitsugu Araki, Yasushi Okuno, Narutoshi Kamiya
Binding Mechanism between Platelet Glycoprotein and Cyclic Peptide Elucidated by McMD-Based Dynamic Docking. Journal of chemical information and modeling 64 (10) (2024)
Gert-Jan Bekker, Mitsugu Araki, Kanji Oshima, Yasushi Okuno, Narutoshi Kamiya
Mutual induced-fit mechanism drives binding between intrinsically disordered Bim and cryptic binding site of Bcl-xL. Communications biology 6 (1) (2023)
Gert-Jan Bekker, Nobutaka Numoto, Maki Kawasaki, Takahiro Hayashi, Saaya Yabuno, Yuko Kozono, Takeyuki Shimizu, Haruo Kozono, Nobutoshi Ito, Masayuki Oda, Narutoshi Kamiya
Elucidation of binding mechanism, affinity and complex structure between mWT1 tumor-associated antigen peptide and HLA-A*24:02. Protein science : a publication of the Protein Society (2023)
Gert-Jan Bekker, Mitsugu Araki, Kanji Oshima, Yasushi Okuno, Narutoshi Kamiya
Mutual induced-fit mechanism drives binding between intrinsically disordered Bim and cryptic binding site of Bcl-xL. Communications biology 6 (1) (2023)
Ryo Kanada, Atsushi Tokuhisa, Yusuke Nagasaka, Shingo Okuno, Koichiro Amemiya, Shuntaro Chiba, Gert-Jan Bekker, Narutoshi Kamiya, Koichiro Kato, Yasushi Okuno
Enhanced Coarse-Grained Molecular Dynamics Simulation with a Smoothed Hybrid Potential Using a Neural Network Model. Journal of chemical theory and computation 20 (1) (2023)
Gert-Jan Bekker, Mitsugu Araki, Kanji Oshima, Yasushi Okuno, Narutoshi Kamiya
Mutual induced-fit mechanism drives binding between intrinsically disordered Bim and cryptic binding site of Bcl-xL. Communications biology 6 (1) (2023)
Ryo Kanada, Atsushi Tokuhisa, Yusuke Nagasaka, Shingo Okuno, Koichiro Amemiya, Shuntaro Chiba, Gert-Jan Bekker, Narutoshi Kamiya, Koichiro Kato, Yasushi Okuno
Enhanced Coarse-Grained Molecular Dynamics Simulation with a Smoothed Hybrid Potential Using a Neural Network Model. Journal of chemical theory and computation (2023)
Gert-Jan Bekker, Mitsugu Araki, Kanji Oshima, Yasushi Okuno, Narutoshi Kamiya
Mutual induced-fit mechanism drives binding between intrinsically disordered Bim and cryptic binding site of Bcl-xL. Communications biology 6 (1) (2023)
Gert-Jan Bekker, Narutoshi Kamiya
Advancing the field of computational drug design using multicanonical molecular dynamics-based dynamic docking. Biophysical reviews 14 (6) (2022)
Gert-Jan Bekker, Narutoshi Kamiya
Advancing the field of computational drug design using multicanonical molecular dynamics-based dynamic docking. Biophysical reviews 14 (6) (2022)
Mitsugu Araki, Shigeyuki Matsumoto, Gert-Jan Bekker, Yuta Isaka, Yukari Sagae, Narutoshi Kamiya, Yasushi Okuno
Exploring ligand binding pathways on proteins using hypersound-accelerated molecular dynamics. Nature communications 12 (1) (2021)
Gert-Jan Bekker, Mitsugu Araki, Kanji Oshima, Yasushi Okuno, Narutoshi Kamiya
Accurate Binding Configuration Prediction of a G-Protein-Coupled Receptor to Its Antagonist Using Multicanonical Molecular Dynamics-Based Dynamic Docking. Journal of chemical information and modeling 61 (10) (2021)
Gert-Jan Bekker, Narutoshi Kamiya
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. The journal of physical chemistry. B (2021)
Gert-Jan Bekker, Takeshi Kawabata, Genji Kurisu
The Biological Structure Model Archive (BSM-Arc): an archive for in silico models and simulations. Biophysical reviews 12 (2) (2020)
Gert-Jan Bekker, Mitsugu Araki, Kanji Oshima, Yasushi Okuno, Narutoshi Kamiya
Exhaustive search of the configurational space of heat-shock protein 90 with its inhibitor by multicanonical molecular dynamics based dynamic docking. Journal of computational chemistry 41 (17) (2020)
Gert-Jan Bekker, Mitsugu Araki, Kanji Oshima, Yasushi Okuno, Narutoshi Kamiya
Dynamic Docking of a Medium-Sized Molecule to Its Receptor by Multicanonical MD Simulations. The journal of physical chemistry. B 123 (11) (2019)
Nobutaka Numoto, Narutoshi Kamiya, Gert-Jan Bekker, Yuri Yamagami, Satomi Inaba, Kentaro Ishii, Susumu Uchiyama, Fusako Kawai, Nobutoshi Ito, Masayuki Oda
Structural Dynamics of the PET-Degrading Cutinase-like Enzyme from Saccharomonospora viridis AHK190 in Substrate-Bound States Elucidates the Ca2+-Driven Catalytic Cycle. Biochemistry 57 (36) (2018)

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Publication Activity (10 Years)

Top Topics

Top Venues

Gert-Jan Bekker