Shun Sakuraba
Shun Sakuraba
Researcher, National Institutes for Quantum and Radiological Science and Technology
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Cited by
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Short synthesis of (+)‐cylindricine C by using a catalytic asymmetric Michael reaction with a two‐center organocatalyst
T Shibuguchi, H Mihara, A Kuramochi, S Sakuraba, T Ohshima, ...
Angewandte Chemie 118 (28), 4751-4753, 2006
ERmod: Fast and versatile computation software for solvation free energy with approximate theory of solutions
S Sakuraba, N Matubayasi
Journal of computational chemistry 35 (21), 1592-1608, 2014
Evaluation of protein-protein docking model structures using all-atom molecular dynamics simulations combined with the solution theory in the energy representation
K Takemura, H Guo, S Sakuraba, N Matubayasi, A Kitao
The Journal of chemical physics 137 (21), 215105, 2012
H3 histone tail conformation within the nucleosome and the impact of K14 acetylation studied using enhanced sampling simulation
J Ikebe, S Sakuraba, H Kono
PLoS computational biology 12 (3), e1004788, 2016
Interaction-component analysis of the hydration and urea effects on cytochrome c
Y Yamamori, R Ishizuka, Y Karino, S Sakuraba, N Matubayasi
The Journal of Chemical Physics 144 (8), 085102, 2016
Detecting coupled collective motions in protein by independent subspace analysis
S Sakuraba, Y Joti, A Kitao
The Journal of chemical physics 133 (18), 11B604, 2010
A theoretical study of the two binding modes between lysozyme and tri-NAG with an explicit solvent model based on the fragment molecular orbital method
T Ishikawa, RR Burri, YO Kamatari, S Sakuraba, N Matubayasi, A Kitao, ...
Physical Chemistry Chemical Physics 15 (10), 3646-3654, 2013
Molecular binding sites are located near the interface of intrinsic dynamics domains (IDDs)
H Li, S Sakuraba, A Chandrasekaran, LW Yang
Journal of chemical information and modeling 54 (8), 2275-2285, 2014
Adaptive lambda square dynamics simulation: An efficient conformational sampling method for biomolecules
J Ikebe, S Sakuraba, H Kono
Journal of Computational Chemistry 35 (1), 39-50, 2014
NMR-NOE and MD simulation study on phospholipid membranes: dependence on membrane diameter and multiple time scale dynamics
M Shintani, K Yoshida, S Sakuraba, M Nakahara, N Matubayasi
The Journal of Physical Chemistry B 115 (29), 9106-9115, 2011
Distribution-function approach to free energy computation
S Sakuraba, N Matubayasi
The Journal of chemical physics 135 (11), 09B607, 2011
Multiple Markov transition matrix method: Obtaining the stationary probability distribution from multiple simulations
S Sakuraba, A Kitao
Journal of computational chemistry 30 (12), 1850-1858, 2009
Free energy profiles for unwrapping the outer superhelical turn of nucleosomal DNA
H Kono, S Sakuraba, H Ishida
PLoS computational biology 14 (3), e1006024, 2018
Enhanced sampling of molecular dynamics simulations of a polyalanine octapeptide: effects of the periodic boundary conditions on peptide conformation
K Kasahara, S Sakuraba, I Fukuda
The Journal of Physical Chemistry B 122 (9), 2495-2503, 2018
Spotting the difference in molecular dynamics simulations of biomolecules
S Sakuraba, H Kono
The Journal of Chemical Physics 145 (7), 074116, 2016
Predicting RNA duplex dimerization free-energy changes upon mutations using molecular dynamics simulations
S Sakuraba, K Asai, T Kameda
The journal of physical chemistry letters 6 (21), 4348-4351, 2015
Free-energy analysis of lysozyme–triNAG binding modes with all-atom molecular dynamics simulation combined with the solution theory in the energy representation
K Takemura, RR Burri, T Ishikawa, T Ishikura, S Sakuraba, N Matubayasi, ...
Chemical Physics Letters 559, 94-98, 2013
A common allosteric mechanism regulates homeostatic inactivation of auxin and gibberellin
S Takehara, S Sakuraba, B Mikami, H Yoshida, H Yoshimura, A Itoh, ...
Nature Communications 11 (1), 1-10, 2020
Critical roles for coiled-coil dimers of butyrophilin 3A1 in the sensing of prenyl pyrophosphates by human Vγ2Vδ2 T cells
H Wang, MH Nada, Y Tanaka, S Sakuraba, CT Morita
The Journal of Immunology 203 (3), 607-626, 2019
Disulfide bond formation of thiols by using carbon nanotubes
A Hirano, T Kameda, S Sakuraba, M Wada, T Tanaka, H Kataura
Nanoscale 9 (17), 5389-5393, 2017
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