フォロー
Chigusa Kobayashi
Chigusa Kobayashi
RIKEN, R-CCS
確認したメール アドレス: riken.go.jp
タイトル
引用先
引用先
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
1762015
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
1542017
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
1192019
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
762000
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
512021
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
512017
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
462021
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
431996
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
412019
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
402022
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
382022
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
382010
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
372006
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
362016
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
342003
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
342001
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
322016
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
282006
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
252016
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
202021
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