| GENESIS: a hybrid‐parallel and multi‐scale molecular dynamics simulator with enhanced sampling algorithms for biomolecular and cellular simulations J Jung, T Mori, C Kobayashi, Y Matsunaga, T Yoda, M Feig, Y Sugita Wiley Interdisciplinary Reviews: Computational Molecular Science 5 (4), 310-323, 2015 | 179 | 2015 |
| GENESIS 1.1: A hybrid‐parallel molecular dynamics simulator with enhanced sampling algorithms on multiple computational platforms C Kobayashi, J Jung, Y Matsunaga, T Mori, T Ando, K Tamura, M Kamiya, ... Journal of Computational Chemistry 38 (25), 2193-2206, 2017 | 156 | 2017 |
| Scaling molecular dynamics beyond 100,000 processor cores for large‐scale biophysical simulations J Jung, W Nishima, M Daniels, G Bascom, C Kobayashi, A Adedoyin, ... Journal of computational chemistry 40 (21), 1919-1930, 2019 | 119 | 2019 |
| Mechanism of fast proton transfer in ice: Potential energy surface and reaction coordinate analyses C Kobayashi, S Saito, I Ohmine The Journal of Chemical Physics 113 (20), 9090-9100, 2000 | 76 | 2000 |
| Elucidation of interactions regulating conformational stability and dynamics of SARS-CoV-2 S-protein T Mori, J Jung, C Kobayashi, HM Dokainish, S Re, Y Sugita Biophysical journal 120 (6), 1060-1071, 2021 | 53 | 2021 |
| Flexible fitting to cryo‐EM density map using ensemble molecular dynamics simulations O Miyashita, C Kobayashi, T Mori, Y Sugita, F Tama Journal of computational chemistry 38 (16), 1447-1461, 2017 | 51 | 2017 |
| New parallel computing algorithm of molecular dynamics for extremely huge scale biological systems J Jung, C Kobayashi, K Kasahara, C Tan, A Kuroda, K Minami, S Ishiduki, ... Journal of computational chemistry 42 (4), 231-241, 2021 | 47 | 2021 |
| Dynamics of proton attachment to water cluster: Proton transfer, evaporation, and relaxation C Kobayashi, K Iwahashi, S Saito, I Ohmine The Journal of chemical physics 105 (15), 6358-6366, 1996 | 43 | 1996 |
| The inherent flexibility of receptor binding domains in SARS-CoV-2 spike protein HM Dokainish, S Re, T Mori, C Kobayashi, J Jung, Y Sugita Elife 11, e75720, 2022 | 42 | 2022 |
| Anharmonic vibrational analysis of biomolecules and solvated molecules using hybrid QM/MM computations K Yagi, K Yamada, C Kobayashi, Y Sugita Journal of Chemical Theory and Computation 15 (3), 1924-1938, 2019 | 41 | 2019 |
| Implementation of residue-level coarse-grained models in GENESIS for large-scale molecular dynamics simulations C Tan, J Jung, C Kobayashi, DUL Torre, S Takada, Y Sugita PLOS Computational Biology 18 (4), e1009578, 2022 | 38 | 2022 |
| Relation between the conformational heterogeneity and reaction cycle of Ras: molecular simulation of Ras C Kobayashi, S Saito Biophysical journal 99 (11), 3726-3734, 2010 | 38 | 2010 |
| Protein grabs a ligand by extending anchor residues: molecular simulation for Ca2+ binding to calmodulin loop C Kobayashi, S Takada Biophysical journal 90 (9), 3043-3051, 2006 | 37 | 2006 |
| Parallel implementation of 3D FFT with volumetric decomposition schemes for efficient molecular dynamics simulations J Jung, C Kobayashi, T Imamura, Y Sugita Computer Physics Communications 200, 57-65, 2016 | 36 | 2016 |
| Multiple versus single pathways in electron transfer in proteins: Influence of protein dynamics and hydrogen bonds C Kobayashi, K Baldridge, JN Onuchic The Journal of chemical physics 119 (6), 3550-3558, 2003 | 34 | 2003 |
| Mechanism of proton transfer in ice. II. Hydration, modes, and transport C Kobayashi, S Saito, I Ohmine The Journal of Chemical Physics 115 (10), 4742-4749, 2001 | 34 | 2001 |
| Dimensionality of collective variables for describing conformational changes of a multi-domain protein Y Matsunaga, Y Komuro, C Kobayashi, J Jung, T Mori, Y Sugita The Journal of Physical Chemistry Letters 7 (8), 1446-1451, 2016 | 32 | 2016 |
| Exploring biomolecular machines: energy landscape control of biological reactions JN Onuchic, C Kobayashi, O Miyashita, P Jennings, KK Baldridge Philosophical Transactions of the Royal Society B: Biological Sciences 361 …, 2006 | 28 | 2006 |
| Graphics processing unit acceleration and parallelization of GENESIS for large-scale molecular dynamics simulations J Jung, A Naurse, C Kobayashi, Y Sugita Journal of Chemical Theory and Computation 12 (10), 4947-4958, 2016 | 25 | 2016 |
| Optimized hydrogen mass repartitioning scheme combined with accurate temperature/pressure evaluations for thermodynamic and kinetic properties of biological systems J Jung, K Kasahara, C Kobayashi, H Oshima, T Mori, Y Sugita Journal of Chemical Theory and Computation 17 (8), 5312-5321, 2021 | 20 | 2021 |
Yuji SugitaRIKENVerified email at riken.go.jp
