Bekker Gerardus Gertrudis Theodorus Bernardus ＢｅｋｋｅｒＧｅｒａｒｄｕ

… Alternative Names

Bekker Gerardu ベッカーゲラルダス

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Researcher Number	80813758
Other IDs	https://orcid.org/0000-0001-8385-5693
Affiliation (Current)	2024: 大阪大学, 蛋白質研究所, 特任講師(常勤)
Affiliation (based on the past Project Information) *help	2020 – 2022: 大阪大学, 蛋白質研究所, 特任助教(常勤)
Review Section/Research Field	Principal Investigator Basic Section 43040:Biophysics-related Except Principal Investigator Basic Section 43040:Biophysics-related
Keywords	Principal Investigator Protein stability / Molecular Dynamics Except Principal Investigator 親和性予測 / 構造予測 / 分子動力学シミュレーション

Development of a database of protein dynamics to elucidate key molecular contributions to stability and affinityPrincipal Investigator
- Principal Investigator
  
  Bekker Gerardu
- Project Period (FY)
  2020 – 2022
- Research Category
  
  Grant-in-Aid for Early-Career Scientists
- Review Section
  
  Basic Section 43040:Biophysics-related
- Research Institution
  Osaka University
Complex structure and affinity prediction among cancer vaccine peptides and immune related proteins
- Principal Investigator
  
  Kamiya Narutoshi
- Project Period (FY)
  2020 – 2022
- Research Category
  
  Grant-in-Aid for Scientific Research (B)
- Review Section
  
  Basic Section 43040:Biophysics-related
- Research Institution
  University of Hyogo

All 2023 2022 2021 2020

All Journal Article

[Journal Article] Mutual induced-fit mechanism drives binding between intrinsically disordered Bim and cryptic binding site of Bcl-xL2023
- Author(s)
  Bekker Gert-Jan、Araki Mitsugu、Oshima Kanji、Okuno Yasushi、Kamiya Narutoshi
- Journal Title
  
  Communications Biology
  
  Volume: 6 Issue: 1 Pages: 349-349
- DOI
  10.1038/s42003-023-04720-6
- Peer Reviewed / Open Access
- Data Source
  KAKENHI-PROJECT-20H03229
[Journal Article] Thermal Stability Estimation of Single Domain Antibodies Using Molecular Dynamics Simulations2022
- Author(s)
  Bekker Gert-Jan、Kamiya Narutoshi
- Journal Title
  
  Methods in Molecular Biology
  
  Volume: 2552 Pages: 151-163
- DOI
  10.1007/978-1-0716-2609-2_8
- ISBN
  9781071626085, 9781071626092
- Data Source
  KAKENHI-PROJECT-20H03229
[Journal Article] Advancing the field of computational drug design using multicanonical molecular dynamics-based dynamic docking2022
- Author(s)
  Bekker Gert-Jan、Kamiya Narutoshi
- Journal Title
  
  Biophysical Reviews
  
  Volume: 14 Issue: 6 Pages: 1349-1358
- DOI
  10.1007/s12551-022-01010-z
- Peer Reviewed
- Data Source
  KAKENHI-PROJECT-20H03229
[Journal Article] Dynamical Methods to Study Interaction in Proteins Facilitating Molecular Understanding of Cancer2021
- Author(s)
  Dasgupta Bhaskar、Bekker Gert-Jan、Kamiya Narutoshi
- Journal Title
  
  Handbook of Oxidative Stress in Cancer: Mechanistic Aspects
  
  Volume: - Pages: 1-17
- DOI
  10.1007/978-981-15-4501-6_149-1
- ISBN
  9789811545016
- Peer Reviewed
- Data Source
  KAKENHI-PROJECT-20H03229
[Journal Article] Accurate Binding Configuration Prediction of a G-Protein-Coupled Receptor to Its Antagonist Using Multicanonical Molecular Dynamics-Based Dynamic Docking2021
- Author(s)
  Bekker Gert-Jan、Araki Mitsugu、Oshima Kanji、Okuno Yasushi、Kamiya Narutoshi
- Journal Title
  
  Journal of Chemical Information and Modeling
  
  Volume: 61 Issue: 10 Pages: 5161-5171
- DOI
  10.1021/acs.jcim.1c00712
- Peer Reviewed
- Data Source
  KAKENHI-PROJECT-20H03229
[Journal Article] Dynamic Docking Using Multicanonical Molecular Dynamics: Simulating Complex Formation at the Atomistic Level2021
- Author(s)
  Bekker Gert-Jan、Kamiya Narutoshi
- Journal Title
  
  Methods in Molecular Biology
  
  Volume: - Pages: 187-202
- DOI
  10.1007/978-1-0716-1209-5_11
- ISBN
  9781071612088, 9781071612095
- Peer Reviewed
- Data Source
  KAKENHI-PROJECT-20H03229
[Journal Article] Cutinases from thermophilic bacteria (actinomycetes): From identification to functional and structural characterization2021
- Author(s)
  Oda Masayuki、Numoto Nobutaka、Bekker Gert-Jan、Kamiya Narutoshi、Kawai Fusako
- Journal Title
  
  Methods in Enzymology
  
  Volume: - Pages: 159-185
- DOI
  10.1016/bs.mie.2020.12.031
- ISBN
  9780128220122
- Peer Reviewed
- Data Source
  KAKENHI-PROJECT-20H03229
[Journal Article] Exploring ligand binding pathways on proteins using hypersound-accelerated molecular dynamics2021
- Author(s)
  Araki Mitsugu、Matsumoto Shigeyuki、Bekker Gert-Jan、Isaka Yuta、Sagae Yukari、Kamiya Narutoshi、Okuno Yasushi
- Journal Title
  
  Nature Communications
  
  Volume: 12 Issue: 1 Pages: 1-10
- DOI
  10.1038/s41467-021-23157-1
- NAID
  120007041708
- Peer Reviewed / Open Access
- Data Source
  KAKENHI-PROJECT-18K06594, KAKENHI-PROJECT-20H03229, KAKENHI-PROJECT-21K06510
[Journal Article] 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 Simulations2021
- Author(s)
  Bekker Gert-Jan、Kamiya Narutoshi
- Journal Title
  
  The Journal of Physical Chemistry B
  
  Volume: 125 Issue: 49 Pages: 13376-13384
- DOI
  10.1021/acs.jpcb.1c07230
- Peer Reviewed
- Data Source
  KAKENHI-PROJECT-20H03229
[Journal Article] Cryptic-site binding mechanism of medium-sized Bcl-xL inhibiting compounds elucidated by McMD-based dynamic docking simulations2021
- Author(s)
  Bekker Gert-Jan、Fukuda Ikuo、Higo Junichi、Fukunishi Yoshifumi、Kamiya Narutoshi
- Journal Title
  
  Scientific Reports
  
  Volume: 11 Issue: 1 Pages: 5046-5046
- DOI
  10.1038/s41598-021-84488-z
- Peer Reviewed / Open Access
- Data Source
  KAKENHI-PROJECT-20H03229
[Journal Article] Exhaustive search of the configurational space of heat‐shock protein 90 with its inhibitor by multicanonical molecular dynamics based dynamic docking2020
- Author(s)
  Bekker Gert‐Jan、Araki Mitsugu、Oshima Kanji、Okuno Yasushi、Kamiya Narutoshi
- Journal Title
  
  Journal of Computational Chemistry
  
  Volume: 41 Issue: 17 Pages: 1606-1615
- DOI
  10.1002/jcc.26203
- Peer Reviewed
- Data Source
  KAKENHI-PROJECT-20H03229
[Journal Article] Structural basis of mutants of <scp>PET</scp> ‐degrading enzyme from <i>Saccharomonospora viridis</i> <scp>AHK190</scp> with high activity and thermal stability2020
- Author(s)
  Emori Miho、Numoto Nobutaka、Senga Akane、Bekker Gert‐Jan、Kamiya Narutoshi、Kobayashi Yuma、Ito Nobutoshi、Kawai Fusako、Oda Masayuki
- Journal Title
  
  Proteins: Structure, Function, and Bioinformatics
  
  Volume: 89 Issue: 5 Pages: 502-511
- DOI
  10.1002/prot.26034
- Peer Reviewed
- Data Source
  KAKENHI-PROJECT-20H03229

1. Kamiya Narutoshi (80420462)

# of Collaborated Projects: 1 results

# of Collaborated Products: 11 results
2. 織田昌幸 (20318231)

# of Collaborated Projects: 1 results

# of Collaborated Products: 2 results
3. 伊藤暢聡 (40361703)

# of Collaborated Projects: 1 results

# of Collaborated Products: 1 results
4. 荒木望嗣

# of Collaborated Projects: 0 results

# of Collaborated Products: 1 results

Bekker Gerardus Gertrudis Theodorus Bernardus Ｂｅｋｋｅｒ Ｇｅｒａｒｄｕ

Bekker Gerardu ベッカー ゲラルダス

Research Projects

Research Products

Co-Researchers

Development of a database of protein dynamics to elucidate key molecular contributions to stability and affinityPrincipal Investigator

Principal Investigator

Project Period (FY)

Research Category

Review Section

Research Institution

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

Principal Investigator

Project Period (FY)

Research Category

Review Section

Research Institution

[Journal Article] Mutual induced-fit mechanism drives binding between intrinsically disordered Bim and cryptic binding site of Bcl-xL2023

Author(s)

Journal Title

DOI

Data Source

[Journal Article] Thermal Stability Estimation of Single Domain Antibodies Using Molecular Dynamics Simulations2022

Author(s)

Journal Title

DOI

ISBN

Data Source

[Journal Article] Advancing the field of computational drug design using multicanonical molecular dynamics-based dynamic docking2022

Author(s)

Journal Title

DOI

Data Source

[Journal Article] Dynamical Methods to Study Interaction in Proteins Facilitating Molecular Understanding of Cancer2021

Author(s)

Journal Title

DOI

ISBN

Data Source

[Journal Article] Accurate Binding Configuration Prediction of a G-Protein-Coupled Receptor to Its Antagonist Using Multicanonical Molecular Dynamics-Based Dynamic Docking2021

Author(s)

Journal Title

DOI

Data Source

[Journal Article] Dynamic Docking Using Multicanonical Molecular Dynamics: Simulating Complex Formation at the Atomistic Level2021

Author(s)

Journal Title

DOI

ISBN

Data Source

[Journal Article] Cutinases from thermophilic bacteria (actinomycetes): From identification to functional and structural characterization2021

Author(s)

Journal Title

DOI

ISBN

Data Source

[Journal Article] Exploring ligand binding pathways on proteins using hypersound-accelerated molecular dynamics2021

Author(s)

Journal Title

DOI

NAID

Data Source

[Journal Article] 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 Simulations2021

Author(s)

Journal Title

DOI

Data Source

[Journal Article] Cryptic-site binding mechanism of medium-sized Bcl-xL inhibiting compounds elucidated by McMD-based dynamic docking simulations2021

Author(s)

Journal Title

DOI

Data Source

[Journal Article] Exhaustive search of the configurational space of heat‐shock protein 90 with its inhibitor by multicanonical molecular dynamics based dynamic docking2020

Author(s)

Journal Title

DOI

Data Source

[Journal Article] Structural basis of mutants of <scp>PET</scp> ‐degrading enzyme from <i>Saccharomonospora viridis</i> <scp>AHK190</scp> with high activity and thermal stability2020

Author(s)

Journal Title

Bekker Gerardus Gertrudis Theodorus Bernardus ＢｅｋｋｅｒＧｅｒａｒｄｕ

Bekker Gerardu ベッカーゲラルダス