| Protein Data Bank: the single global archive for 3D macromolecular structure data Nucleic acids research 47 (D1), D520-D528, 2019 | 635 | 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 | 137 | 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 | 76 | 2018 |
| 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 | 73 | 2018 |
| Molmil: a molecular viewer for the PDB and beyond GJ Bekker, H Nakamura, AR Kinjo Journal of cheminformatics 8 (1), 1-5, 2016 | 64 | 2016 |
| Thermal stability of single‐domain antibodies estimated by molecular dynamics simulations GJ Bekker, B Ma, N Kamiya Protein Science 28 (2), 429-438, 2019 | 49 | 2019 |
| 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 | 46 | 2017 |
| 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 | 42 | 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 | 36 | 2020 |
| 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, 2655-2663, 2019 | 36 | 2019 |
| 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 | 35 | 2022 |
| 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), 2793, 2021 | 28 | 2021 |
| 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 | 23 | 2019 |
| 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 | 21 | 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 | 21 | 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 | 21 | 2018 |
| 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 | 17 | 2019 |
| 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), 5046, 2021 | 12 | 2021 |
| Accurate Binding Configuration Prediction of a G-Protein-Coupled Receptor to Its Antagonist Using Multicanonical Molecular Dynamics-Based Dynamic Docking GJ Bekker, M Araki, K Oshima, Y Okuno, N Kamiya Journal of Chemical Information and Modeling 61 (10), 5161-5171, 2021 | 11 | 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 | 10 | 2021 |
