| 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 | 877 | 2002 |
| 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 | 429 | 2001 |
| 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 | 377 | 2008 |
| 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 | 347 | 2006 |
| 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 | 306 | 2009 |
| 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 | 255 | 2003 |
| Coarse-grained molecular simulations of large biomolecules S Takada Current opinion in structural biology 22 (2), 130-137, 2012 | 251 | 2012 |
| 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 | 223 | 1999 |
| 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 | 213 | 2011 |
| 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 | 194 | 2001 |
| Gō-ing for the prediction of protein folding mechanisms S Takada Proceedings of the National Academy of Sciences 96 (21), 11698-11700, 1999 | 186 | 1999 |
| 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 | 167 | 2011 |
| 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 | 165 | 2011 |
| Energy landscape views for interplays among folding, binding, and allostery of calmodulin domains W Li, W Wang, S Takada Proceedings of the National Academy of Sciences 111 (29), 10550-10555, 2014 | 153 | 2014 |
| 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 | 147 | 2012 |
| Modeling structural dynamics of biomolecular complexes by coarse-grained molecular simulations S Takada, R Kanada, C Tan, T Terakawa, W Li, H Kenzaki Accounts of chemical research 48 (12), 3026-3035, 2015 | 137 | 2015 |
| Variational theory for site resolved protein folding free energy surfaces JJ Portman, S Takada, PG Wolynes Physical review letters 81 (23), 5237, 1998 | 137 | 1998 |
| 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 | 133 | 2006 |
| 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 | 131 | 1995 |
| 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 | 124 | 2004 |
Peter G. WolynesBullard-Welch Foundation Professor of Science, Professor of Chemistry, Professor of PhysicsVerified email at rice.edu
