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Yasuhiro Matsunaga
Yasuhiro Matsunaga
Verified email at mail.saitama-u.ac.jp
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Year
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
1882015
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
1632017
Minimum free energy path of ligand-induced transition in adenylate kinase
Y Matsunaga, H Fujisaki, T Terada, T Furuta, K Moritsugu, A Kidera
PLoS computational biology 8 (6), e1002555, 2012
1072012
How many dimensions are required to approximate the potential energy landscape of a model protein?
T Komatsuzaki, K Hoshino, Y Matsunaga, GJ Rylance, RL Johnston, ...
The Journal of chemical physics 122 (8), 2005
652005
Phase-space reaction network on a multisaddle energy landscape: HCN isomerization
CB Li, Y Matsunaga, M Toda, T Komatsuzaki
The Journal of chemical physics 123 (18), 2005
492005
Linking time-series of single-molecule experiments with molecular dynamics simulations by machine learning
Y Matsunaga, Y Sugita
Elife 7, e32668, 2018
482018
Topographical complexity of multidimensional energy landscapes
GJ Rylance, RL Johnston, Y Matsunaga, CB Li, A Baba, T Komatsuzaki
Proceedings of the National Academy of Sciences 103 (49), 18551-18555, 2006
432006
Energetics and conformational pathways of functional rotation in the multidrug transporter AcrB
Y Matsunaga, T Yamane, T Terada, K Moritsugu, H Fujisaki, S Murakami, ...
Elife 7, e31715, 2018
382018
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
342016
Extended phase-space methods for enhanced sampling in molecular simulations: a review
H Fujisaki, K Moritsugu, Y Matsunaga, T Morishita, L Maragliano
Frontiers in bioengineering and biotechnology 3, 125, 2015
282015
Protein functional motions: basic concepts and computational methodologies
S Fuchigami, H Fujisaki, Y Matsunaga, A Kidera
Advancing Theory for Kinetics and Dynamics of Complex, Many‐Dimensional …, 2011
282011
Anomalous diffusion in folding dynamics of minimalist protein landscape
Y Matsunaga, CB Li, T Komatsuzaki
Physical review letters 99 (23), 238103, 2007
202007
Rigid-body fitting to atomic force microscopy images for inferring probe shape and biomolecular structure
T Niina, Y Matsunaga, S Takada
PLOS Computational Biology 17 (7), e1009215, 2021
182021
Influence of structural symmetry on protein dynamics
Y Matsunaga, R Koike, M Ota, JRH Tame, A Kidera
PLoS One 7 (11), e50011, 2012
172012
Regularity in chaotic transitions on multibasin landscapes
T Komatsuzaki, K Hoshino, Y Matsunaga
Geometric Structures of Phase Space in Multidimensional Chaos: Applications …, 2005
172005
Multibasin dynamics in off-lattice minimalist protein landscapes
Y Matsunaga, KS Kostov, T Komatsuzaki
The Journal of Physical Chemistry A 106 (45), 10898-10907, 2002
162002
Structural and energetic analysis of metastable intermediate states in the E1P–E2P transition of Ca2+-ATPase
C Kobayashi, Y Matsunaga, J Jung, Y Sugita
Proceedings of the National Academy of Sciences 118 (40), e2105507118, 2021
152021
Use of single-molecule time-series data for refining conformational dynamics in molecular simulations
Y Matsunaga, Y Sugita
Current opinion in structural biology 61, 153-159, 2020
152020
Non-brownian phase space dynamics of molecules, the nature of their vibrational states, and non-RRKM kinetics
DM Leitner, Y Matsunaga, CB Li, T Komatsuzaki, A Shojiguchi, M Toda
Advances in Chemical Physics 145, 83, 2011
152011
Domain motion enhanced (DoME) model for efficient conformational sampling of multidomain proteins
C Kobayashi, Y Matsunaga, R Koike, M Ota, Y Sugita
The Journal of Physical Chemistry B 119 (46), 14584-14593, 2015
142015
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