Gert-Jan Bekker

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Specially Appointed Lecturer

Osaka University

Japan

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About

Gert-Jan Bekker is a Specially Appointed Lecturer at Osaka University, Japan. His research focuses on protein structures, molecular dynamics, and binding mechanisms, as evidenced by his recent publications, including work on the Protein Data Bank Japan and studies on Ca2+-regulated cutinase and Dihydrofolate Reductase. He is also involved in exploring genetic variants associated with familial episodic pain syndromes and has contributed to advancements in molecular dynamics simulations.

Recent Grants

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Complex structure and affinity prediction among cancer vaccine peptides and immune related proteins

Open Date: 2020-04-01

Close Date: 2023-03-31

Articles (19)

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Collaborators (9)

Kei Yura

Professor

Waseda University

JAPAN

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GENJI KURISU

Professor

Osaka University

JAPAN

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Koichiro Kato

Kyushu University

JAPAN

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Shigeyuki Matsumoto

Kyoto University

JAPAN

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Narutoshi Kamiya

Specially Appointed Professor

University of Hyogo

JAPAN

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Haruki Nakamura

ProfessorEmeritus

Osaka University

JAPAN

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Masayuki Oda

Kyoto University

JAPAN

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Toshiaki Katayama

JAPAN

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Nobutaka Numoto

Special-Appointment Associate Professor

Okayama University

JAPAN

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Gert-Jan Bekker

Research Interests

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About

Recent Grants

Articles (19)

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

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

Familial Episodic Pain Syndrome: A Japanese Family Harboring the Novel Variant c.2431C>T (p.Leu811Phe) in SCN11A

Binding Mechanism between Platelet Glycoprotein and Cyclic Peptide Elucidated by McMD-Based Dynamic Docking

Binding Mechanism of Riboswitch to Natural Ligand Elucidated by McMD-Based Dynamic Docking Simulations

Enhanced Coarse-Grained Molecular Dynamics Simulation with a Smoothed Hybrid Potential Using a Neural Network Model

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

Molecular Dynamics Unveils Multiple-Site Binding of Inhibitors with Reduced Activity on the Surface of Dihydrofolate Reductase

Elucidation of binding mechanism, affinity and complex structure between mWT1 tumor‐associated antigen peptide and HLA‐A*24:02

Mutual induced-fit mechanism drives binding between intrinsically disordered Bim and cryptic binding site of Bcl-xL

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

History of Protein Data Bank Japan: standing at the beginning of the age of structural genomics

Advancing the field of computational drug design using multicanonical molecular dynamics-based dynamic docking

Fly casting with ligand sliding and orientational selection supporting complex formation of a GPCR and a middle sized flexible molecule

Protein Data Bank Japan: Celebrating our 20th anniversary during a global pandemic as the Asian hub of three dimensional macromolecular structural data

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

Accurate Binding Configuration Prediction of a G-Protein-Coupled Receptor to Its Antagonist Using Multicanonical Molecular Dynamics-Based Dynamic Docking

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

Structural basis of mutants of <scp>PET</scp>‐degrading enzyme from <i>Saccharomonospora viridis</i><scp>AHK190</scp> with high activity and thermal stability

Collaborators (9)

Kei Yura

GENJI KURISU

Koichiro Kato

Shigeyuki Matsumoto

Narutoshi Kamiya

Haruki Nakamura

Masayuki Oda

Toshiaki Katayama

Nobutaka Numoto

Make your next move.

Gert-Jan Bekker

Research Interests

Explore related searches

Contact this professor

About

Recent Grants

Articles (19)

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

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

Familial Episodic Pain Syndrome: A Japanese Family Harboring the Novel Variant c.2431C&gt;T (p.Leu811Phe) in SCN11A

Binding Mechanism between Platelet Glycoprotein and Cyclic Peptide Elucidated by McMD-Based Dynamic Docking

Binding Mechanism of Riboswitch to Natural Ligand Elucidated by McMD-Based Dynamic Docking Simulations

Enhanced Coarse-Grained Molecular Dynamics Simulation with a Smoothed Hybrid Potential Using a Neural Network Model

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

Molecular Dynamics Unveils Multiple-Site Binding of Inhibitors with Reduced Activity on the Surface of Dihydrofolate Reductase

Elucidation of binding mechanism, affinity and complex structure between mWT1 tumor‐associated antigen peptide and HLA‐A*24:02

Mutual induced-fit mechanism drives binding between intrinsically disordered Bim and cryptic binding site of Bcl-xL

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

History of Protein Data Bank Japan: standing at the beginning of the age of structural genomics

Advancing the field of computational drug design using multicanonical molecular dynamics-based dynamic docking

Fly casting with ligand sliding and orientational selection supporting complex formation of a GPCR and a middle sized flexible molecule

Protein Data Bank Japan: Celebrating our 20th anniversary during a global pandemic as the Asian hub of three dimensional macromolecular structural data

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

Accurate Binding Configuration Prediction of a G-Protein-Coupled Receptor to Its Antagonist Using Multicanonical Molecular Dynamics-Based Dynamic Docking

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

Structural basis of mutants of <scp>PET</scp>‐degrading enzyme from <i>Saccharomonospora viridis</i><scp>AHK190</scp> with high activity and thermal stability

Collaborators (9)

Kei Yura

GENJI KURISU

Koichiro Kato

Shigeyuki Matsumoto

Narutoshi Kamiya

Haruki Nakamura

Masayuki Oda

Toshiaki Katayama

Nobutaka Numoto

Make your next move.

Familial Episodic Pain Syndrome: A Japanese Family Harboring the Novel Variant c.2431C>T (p.Leu811Phe) in SCN11A