Gert-jan Bekker

Suita, 5650871, Japan

Last Updated: 09/26/2026

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Found 42 publications

Comparative Assessment of DNA Force Fields for Small-Molecule Ligand Binding via Multicanonical MD-Based Dynamic Docking Simulations.

Comparative Assessment of DNA Force Fields for Small-Molecule Ligand Binding via Multicanonical MD-Based Dynamic Docking Simulations.

Journal: Journal of chemical theory and computation

Published: May 28, 2026

Protein Data Bank Japan: A unified portal for integrating structural and chemical data to explore protein-ligand interactions in PDB and PubChem.

Protein Data Bank Japan: A unified portal for integrating structural and chemical data to explore protein-ligand interactions in PDB and PubChem.

Journal: Protein science : a publication of the Protein Society

Published: March 30, 2026

Elucidating Ligand Charge Effects in MR1 Cell-Surface Translocation Using Molecular Simulations.

Elucidating Ligand Charge Effects in MR1 Cell-Surface Translocation Using Molecular Simulations.

Journal: Journal of chemical information and modeling

Published: February 10, 2026

Stability-Driven Pose Prediction and Ligand Design via Contact Persistence Analysis from Molecular Dynamics Simulations.

Stability-Driven Pose Prediction and Ligand Design via Contact Persistence Analysis from Molecular Dynamics Simulations.

Journal: Computational and structural biotechnology journal

Published: December 25, 2025

Uncovering the role of dimerization on dynamics and inhibitor stability in human versus Xenopus LTA4H.

Uncovering the role of dimerization on dynamics and inhibitor stability in human versus Xenopus LTA4H.

Journal: Biophysical journal

Published: November 29, 2025

Assessment of RNA Force Fields for Dynamic Docking of Small Molecules Using Multicanonical MD Simulations.

Assessment of RNA Force Fields for Dynamic Docking of Small Molecules Using Multicanonical MD Simulations.

Journal: Journal of chemical theory and computation

Published: October 22, 2025

Molecular recognition of natural compounds by MR1 and their implication in MAIT cell activation elucidated through McMD-based dynamic docking simulations.

Molecular recognition of natural compounds by MR1 and their implication in MAIT cell activation elucidated through McMD-based dynamic docking simulations.

Journal: Scientific reports

Published: June 29, 2025

Structure-activity relationship of PET-degrading cutinase regulated by weak Ca2+ binding and temperature.

Structure-activity relationship of PET-degrading cutinase regulated by weak Ca2+ binding and temperature.

Journal: Biophysics and physicobiology

Published: March 10, 2025

A virtual system-coupled molecular dynamics simulation free from experimental knowledge on binding sites: Application to RNA-ligand binding free-energy landscape.

A virtual system-coupled molecular dynamics simulation free from experimental knowledge on binding sites: Application to RNA-ligand binding free-energy landscape.

Journal: Biophysics and physicobiology

Published: January 10, 2025

Protein Data Bank Japan: Computational Resources for Analysis of Protein Structures.

Protein Data Bank Japan: Computational Resources for Analysis of Protein Structures.

Journal: Journal of molecular biology

Published: November 29, 2024

Protein Data Bank Japan: Improved tools for sequence-oriented analysis of protein structures.

Protein Data Bank Japan: Improved tools for sequence-oriented analysis of protein structures.

Journal: Protein science : a publication of the Protein Society

Published: November 02, 2024

Structural dynamics of the Ca2+-regulated cutinase towards structure-based improvement of PET degradation activity.

Structural dynamics of the Ca2+-regulated cutinase towards structure-based improvement of PET degradation activity.

Journal: International journal of biological macromolecules

Published: July 08, 2024

Showing 1-12 of 42

Last Updated: 09/26/2026