Gert-Jan Bekker
Gert-Jan Bekker
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Protein Data Bank: the single global archive for 3D macromolecular structure data
Nucleic acids research 47 (D1), D520-D528, 2019
Protein Data Bank Japan (PDBj): updated user interfaces, resource description framework, analysis tools for large structures
AR Kinjo, GJ Bekker, H Suzuki, Y Tsuchiya, T Kawabata, Y Ikegawa, ...
Nucleic acids research, gkw962, 2016
New tools and functions in data‐out activities at Protein Data Bank Japan (PDBj)
AR Kinjo, GJ Bekker, H Wako, S Endo, Y Tsuchiya, H Sato, H Nishi, ...
Protein Science 27 (1), 95-102, 2018
Molmil: a molecular viewer for the PDB and beyond
GJ Bekker, H Nakamura, AR Kinjo
Journal of cheminformatics 8 (1), 1-5, 2016
Structural Dynamics of the PET-Degrading Cutinase-like Enzyme from Saccharomonospora viridis AHK190 in Substrate-Bound States Elucidates the Ca2+-Driven …
N Numoto, N Kamiya, GJ Bekker, Y Yamagami, S Inaba, K Ishii, ...
Biochemistry 57 (36), 5289-5300, 2018
Accurate prediction of complex structure and affinity for a flexible protein receptor and its inhibitor
GJ Bekker, N Kamiya, M Araki, I Fukuda, Y Okuno, H Nakamura
Journal of chemical theory and computation 13 (6), 2389-2399, 2017
Thermal stability of single‐domain antibodies estimated by molecular dynamics simulations
GJ Bekker, B Ma, N Kamiya
Protein Science 28 (2), 429-438, 2019
Folding thermodynamics of PET-hydrolyzing enzyme Cut190 depending on Ca2+ concentration
S Inaba, N Kamiya, GJ Bekker, F Kawai, M Oda
Journal of Thermal Analysis and Calorimetry 135 (5), 2655-2663, 2019
The Biological Structure Model Archive (BSM-Arc): an archive for in silico models and simulations
GJ Bekker, T Kawabata, G Kurisu
Biophysical Reviews, 1-5, 2020
Mutual population-shift driven antibody-peptide binding elucidated by molecular dynamics simulations
GJ Bekker, I Fukuda, J Higo, N Kamiya
Scientific Reports 10 (1), 1406, 2020
Structural and thermodynamic characterization of endo-1, 3-β-glucanase: Insights into the substrate recognition mechanism
M Oda, S Inaba, N Kamiya, GJ Bekker, B Mikami
Biochimica et Biophysica Acta (BBA)-Proteins and Proteomics 1866 (3), 415-425, 2018
Dynamic Docking of a Medium-Sized Molecule to Its Receptor by Multicanonical MD Simulations
GJ Bekker, M Araki, K Oshima, Y Okuno, N Kamiya
The Journal of Physical Chemistry B 123 (11), 2479-2490, 2019
Metal binding to cutinase-like enzyme from Saccharomonospora viridis AHK190 and its effects on enzyme activity and stability
A Senga, Y Hantani, GJ Bekker, N Kamiya, Y Kimura, F Kawai, M Oda
The Journal of Biochemistry 166 (2), 149-156, 2019
Exploring ligand binding pathways on proteins using hypersound-accelerated molecular dynamics
M Araki, S Matsumoto, GJ Bekker, Y Isaka, Y Sagae, N Kamiya, Y Okuno
Nature communications 12 (1), 1-10, 2021
Exhaustive search of the configurational space of heat‐shock protein 90 with its inhibitor by multicanonical molecular dynamics based dynamic docking
GJ Bekker, M Araki, K Oshima, Y Okuno, N Kamiya
Journal of Computational Chemistry 41 (17), 1606-1615, 2020
Structural basis of mutants of PET‐degrading enzyme from Saccharomonospora viridis AHK190 with high activity and thermal stability
M Emori, N Numoto, A Senga, GJ Bekker, N Kamiya, Y Kobayashi, N Ito, ...
Proteins: Structure, Function, and Bioinformatics 89 (5), 502-511, 2021
Cutinases from thermophilic bacteria (actinomycetes): From identification to functional and structural characterization.
M Oda, N Numoto, GJ Bekker, N Kamiya, F Kawai
Methods in Enzymology 648, 159-185, 2021
Protein Data Bank Japan: Celebrating our 20th anniversary during a global pandemic as the Asian hub of three dimensional macromolecular structural data
GJ Bekker, M Yokochi, H Suzuki, Y Ikegawa, T Iwata, T Kudou, K Yura, ...
Protein Science 31 (1), 173-186, 2022
Cryptic-site binding mechanism of medium-sized Bcl-xL inhibiting compounds elucidated by McMD-based dynamic docking simulations
GJ Bekker, I Fukuda, J Higo, Y Fukunishi, N Kamiya
Scientific Reports 11 (1), 1-12, 2021
Dynamic docking using multicanonical molecular dynamics: Simulating complex formation at the atomistic level
GJ Bekker, N Kamiya
Protein-Ligand Interactions and Drug Design, 187-202, 2021
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