Shoji Takada
Shoji Takada
Verified email at biophys.kyoto-u.ac.jp
TitleCited byYear
On the Hamiltonian replica exchange method for efficient sampling of biomolecular systems: application to protein structure prediction
H Fukunishi, O Watanabe, S Takada
The Journal of chemical physics 116 (20), 9058-9067, 2002
6452002
Roles of native topology and chain-length scaling in protein folding: a simulation study with a Gō-like model
N Koga, S Takada
Journal of molecular biology 313 (1), 171-180, 2001
3902001
Dynamic energy landscape view of coupled binding and protein conformational change: induced-fit versus population-shift mechanisms
K Okazaki, S Takada
Proceedings of the National Academy of Sciences 105 (32), 11182-11187, 2008
3012008
Multiple-basin energy landscapes for large-amplitude conformational motions of proteins: Structure-based molecular dynamics simulations
K Okazaki, N Koga, S Takada, JN Onuchic, PG Wolynes
Proceedings of the National Academy of Sciences 103 (32), 11844-11849, 2006
2662006
How protein thermodynamics and folding mechanisms are altered by the chaperonin cage: molecular simulations
F Takagi, N Koga, S Takada
Proceedings of the National Academy of Sciences 100 (20), 11367-11372, 2003
2372003
Folding dynamics with nonadditive forces: a simulation study of a designed helical protein and a random heteropolymer
S Takada, Z Luthey-Schulten, PG Wolynes
The Journal of chemical physics 110 (23), 11616-11629, 1999
2111999
Coarse-grained molecular simulations of large biomolecules
S Takada
Current opinion in structural biology 22 (2), 130-137, 2012
1762012
Gō-ing for the prediction of protein folding mechanisms
S Takada
Proceedings of the National Academy of Sciences 96 (21), 11698-11700, 1999
1761999
Bimodal protein solubility distribution revealed by an aggregation analysis of the entire ensemble of Escherichia coli proteins
T Niwa, BW Ying, K Saito, WZ Jin, S Takada, T Ueda, H Taguchi
Proceedings of the National Academy of Sciences 106 (11), 4201-4206, 2009
1712009
Microscopic theory of protein folding rates. II. Local reaction coordinates and chain dynamics
JJ Portman, S Takada, PG Wolynes
The Journal of Chemical Physics 114 (11), 5082-5096, 2001
1632001
Frustration, specific sequence dependence, and nonlinearity in large-amplitude fluctuations of allosteric proteins
W Li, PG Wolynes, S Takada
Proceedings of the National Academy of Sciences 108 (9), 3504-3509, 2011
1302011
Variational theory for site resolved protein folding free energy surfaces
JJ Portman, S Takada, PG Wolynes
Physical review letters 81 (23), 5237, 1998
1291998
Optimizing physical energy functions for protein folding
Y Fujitsuka, S Takada, ZA Luthey‐Schulten, PG Wolynes
Proteins: Structure, Function, and Bioinformatics 54 (1), 88-103, 2004
1212004
Microscopic theory of protein folding rates. I. Fine structure of the free energy profile and folding routes from a variational approach
JJ Portman, S Takada, PG Wolynes
The Journal of Chemical Physics 114 (11), 5069-5081, 2001
1142001
Folding-based molecular simulations reveal mechanisms of the rotary motor F1–ATPase
N Koga, S Takada
Proceedings of the National Academy of Sciences 103 (14), 5367-5372, 2006
1132006
Effects of vibrational excitation on multidimensional tunneling: General study and proton tunneling in tropolone
S Takada, H Nakamura
The Journal of chemical physics 102 (10), 3977-3992, 1995
1131995
On easy implementation of a variant of the replica exchange with solute tempering in GROMACS
T Terakawa, T Kameda, S Takada
Journal of computational chemistry 32 (7), 1228-1234, 2011
1062011
CafeMol: a coarse-grained biomolecular simulator for simulating proteins at work
H Kenzaki, N Koga, N Hori, R Kanada, W Li, K Okazaki, XQ Yao, ...
Journal of Chemical Theory and Computation 7 (6), 1979-1989, 2011
1032011
Wentzel–Kramers–Brillouin theory of multidimensional tunneling: General theory for energy splitting
S Takada, H Nakamura
The Journal of chemical physics 100 (1), 98-113, 1994
1011994
Energy landscape and multiroute folding of topologically complex proteins adenylate kinase and 2ouf-knot
W Li, T Terakawa, W Wang, S Takada
Proceedings of the National Academy of Sciences 109 (44), 17789-17794, 2012
912012
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Articles 1–20