| 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 | 193 | 2015 |
| Comparisons of force fields for proteins by generalized-ensemble simulations T Yoda, Y Sugita, Y Okamoto Chemical Physics Letters 386 (4-6), 460-467, 2004 | 188 | 2004 |
| Erratum to''Effect of the Extra N-terminal Methionine Residue on the Stability and Folding of Recombinant α-Lactalbumin Expressed in Escherichia coli''[J. Mol. Biol.(1999) 285 … TK Chaudhuri, K Horii, T Yoda, M Arai, S Nagata, TP Terada, H Uchiyama, ... Journal of Molecular Biology 3 (336), 825, 2004 | 118* | 2004 |
| Effect of the extra N-terminal methionine residue on the stability and folding of recombinant α-lactalbumin expressed in Escherichia coli TK Chaudhuri, K Horii, T Yoda, M Arai, S Nagata, TP Terada, H Uchiyama, ... Journal of molecular biology 285 (3), 1179-1194, 1999 | 118 | 1999 |
| Secondary-structure preferences of force fields for proteins evaluated by generalized-ensemble simulations T Yoda, Y Sugita, Y Okamoto Chemical physics 307 (2-3), 269-283, 2004 | 117 | 2004 |
| Cooperative folding mechanism of a β‐hairpin peptide studied by a multicanonical replica‐exchange molecular dynamics simulation T Yoda, Y Sugita, Y Okamoto Proteins: Structure, Function, and Bioinformatics 66 (4), 846-859, 2007 | 68 | 2007 |
| Hydrophobic core formation and dehydration in protein folding studied by generalized-ensemble simulations T Yoda, Y Sugita, Y Okamoto Biophysical journal 99 (5), 1637-1644, 2010 | 49 | 2010 |
| Structural changes in the cytoplasmic domain of phospholamban by phosphorylation at Ser16: a molecular dynamics study Y Sugita, N Miyashita, T Yoda, M Ikeguchi, C Toyoshima Biochemistry 45 (39), 11752-11761, 2006 | 41 | 2006 |
| Localized nature of the transition-state structure in goat α-lactalbumin folding K Saeki, M Arai, T Yoda, M Nakao, K Kuwajima Journal of molecular biology 341 (2), 589-604, 2004 | 34 | 2004 |
| Structures of a peptide fragment of β2-microglobulin studied by replica-exchange molecular dynamics simulations–Towards the understanding of the mechanism of amyloid formation M Nishino, Y Sugita, T Yoda, Y Okamoto FEBS letters 579 (24), 5425-5429, 2005 | 33 | 2005 |
| Folding‐unfolding of goat α‐lactalbumin studied by stopped‐flow circular dichroism and molecular dynamics simulations T Yoda, M Saito, M Arai, K Horii, K Tsumoto, M Matsushima, I Kumagai, ... Proteins: Structure, Function, and Bioinformatics 42 (1), 49-65, 2001 | 19 | 2001 |
| Contribution of Thr29 to the thermodynamic stability of goat α‐lactalbumin as determined by experimental and theoretical approaches K Horii, M Saito, T Yoda, K Tsumoto, M Matsushima, K Kuwajima, ... Proteins: Structure, Function, and Bioinformatics 45 (1), 16-29, 2001 | 17 | 2001 |
| Short disordered protein segment regulates cross-species transmission of a yeast prion T Shida, YO Kamatari, T Yoda, Y Yamaguchi, M Feig, Y Ohhashi, Y Sugita, ... Nature chemical biology 16 (7), 756-765, 2020 | 12 | 2020 |
| Replica-exchange molecular dynamics simulation of diffracted X-ray tracking Y Kawashima, YC Sasaki, Y Sugita, T Yoda, Y Okamoto Molecular Simulation 33 (1-2), 97-102, 2007 | 9 | 2007 |
| Deciphering supramolecular structures with protein-protein interaction network modeling T Tsuji, T Yoda, T Shirai Scientific reports 5 (1), 1-13, 2015 | 8 | 2015 |
| Protein folding simulations by generalized-ensemble algorithms T Yoda, Y Sugita, Y Okamoto Protein Conformational Dynamics, 1-27, 2014 | 8 | 2014 |
| Effects of the fixed end in single-molecule imaging techniques: A replica-exchange molecular dynamics simulation study Y Kawashima, Y Sugita, T Yoda, Y Okamoto Chemical physics letters 414 (4-6), 449-455, 2005 | 8 | 2005 |
| Salt effects on hydrophobic‐core formation in folding of a helical miniprotein studied by molecular dynamics simulations T Yoda, Y Sugita, Y Okamoto Proteins: Structure, Function, and Bioinformatics 82 (6), 933-943, 2014 | 7 | 2014 |
| Recent applications of replica-exchange molecular dynamics simulations of biomolecules Y Sugita, N Miyashita, PC Li, T Yoda, Y Okamoto Current Physical Chemistry 2 (4), 401-412, 2012 | 5 | 2012 |
| Exonuclease processivity of archaeal replicative DNA polymerase in association with PCNA is expedited by mismatches in DNA T Yoda, M Tanabe, T Tsuji, T Yoda, S Ishino, T Shirai, Y Ishino, ... Scientific reports 7 (1), 1-14, 2017 | 3 | 2017 |
