Author

G.-J. Bekker

Listed by name: these papers carry no ORCID for this author, so different people with the same name may be mixed together.

Biology Disciplines

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Biophysics· 4

Signature Assays, Organisms & Methods

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Research Focus:drug response / drug discovery· 2 Approach:mechanistic / dynamical model· 2 Research Focus:protein folding & dynamics· 2 Assay:protein structure· 2 Research Focus:cell signaling & trafficking· 1 Research Focus:chromatin & epigenetic regulation· 1 Approach:deep learning· 1 Approach:experimental assay· 1

Frequent Co-Authors

N. Kamiya· 4 shared I. Fukuda· 2 shared J. Higo· 2 shared M. Araki· 2 shared S. Matsumoto· 2 shared Y. Fukunishi· 2 shared Y. Isaka· 2 shared Y. Okuno· 2 shared

Activity by Year

2020-2024 · peak 1/yr

Co-Author Collaboration Network

10 top collaborators · 25 mutual co-author links

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4 shared papersBiophysics

N. Kamiya

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Author profile →

4 papers

Recent·Most cited

Molecular dynamics unveils multiple-site binding of inhibitors with reduced activity on the surface of dihydrofolate reductase

M. Araki, T. Ekimoto, K. Takemura, S. Matsumoto, Y. Tamura, H. Kokubo, G.-J. Bekker, T. Yamane, Y. Isaka, Y. Sagae, N. Kamiya, M. Ikeguchi, Y. Okuno

This study uses molecular dynamics to analyze inhibitor binding to DHFR, showing that reduced activity correlates with multiple-bound states on the protein surface.

bioRxiv · Mar 27, 2024Biophysics

Binding free-energy landscapes of small molecule binder and non-binder to FMN riboswitch: All-atom molecular dynamics

J. Higo, G.-J. Bekker, N. Kamiya, I. Fukuda, Y. Fukunishi

This study uses molecular dynamics to compare binding free-energy landscapes of two structurally similar ligands to an FMN riboswitch, revealing distinct binding pathways and orientation effects.

bioRxiv · Jul 1, 2023Biophysics

Fly-casting with ligand-sliding and orientational selection to support the complex formation of a GPCR and a middle-sized flexible molecule

J. Higo, K. Kasahara, G.-J. Bekker, B. Ma, S. Sakuraba, S. Iida, N. Kamiya, I. Fukuda, H. Kono, Y. Fukunishi, H. Nakamura

This paper uses a computational method to simulate the binding mechanism of bosentan to hETB, identifying key steps like fly-casting and ligand-sliding.

bioRxiv · Feb 28, 2022 · PreprintBiophysics

Exploring ligand binding pathways on proteins using hypersound-accelerated molecular dynamics

M. Araki, S. Matsumoto, G.-J. Bekker, Y. Isaka, Y. Sagae, N. Kamiya, Y. Okuno

This study accelerates molecular dynamics simulations using ultrasound to study ligand binding pathways on proteins, revealing previously undetectable kinetic features and binding pathways.

bioRxiv · Apr 6, 2020Biophysics