| Binding of an RNA aptamer and a partial peptide of a prion protein: crucial importance of water entropy in molecular recognition T Hayashi, H Oshima, T Mashima, T Nagata, M Katahira, M Kinoshita Nucleic acids research 42 (11), 6861-6875, 2014 | 103 | 2014 |
| CHARMM-GUI free energy calculator for absolute and relative ligand solvation and binding free energy simulations S Kim, H Oshima, H Zhang, NR Kern, S Re, J Lee, B Roux, Y Sugita, ... Journal of chemical theory and computation 16 (11), 7207-7218, 2020 | 102 | 2020 |
| Replica-exchange umbrella sampling combined with Gaussian accelerated molecular dynamics for free-energy calculation of biomolecules H Oshima, S Re, Y Sugita Journal of Chemical Theory and Computation 15 (10), 5199-5208, 2019 | 84 | 2019 |
| Effects of sugars on the thermal stability of a protein H Oshima, M Kinoshita Biophysical Journal 104 (2), 563a, 2013 | 66 | 2013 |
| Essential roles of protein-solvent many-body correlation in solvent-entropy effect on protein folding and denaturation: Comparison between hard-sphere solvent and water H Oshima, M Kinoshita The Journal of chemical physics 142 (14), 2015 | 64 | 2015 |
| Encounter complexes and hidden poses of kinase-inhibitor binding on the free-energy landscape S Re, H Oshima, K Kasahara, M Kamiya, Y Sugita Proceedings of the National Academy of Sciences 116 (37), 18404-18409, 2019 | 54 | 2019 |
| Effects of side-chain packing on the formation of secondary structures in protein folding S Yasuda, T Yoshidome, H Oshima, R Kodama, Y Harano, M Kinoshita The Journal of chemical physics 132 (6), 2010 | 51 | 2010 |
| A theoretical analysis on characteristics of protein structures induced by cold denaturation H Oshima, T Yoshidome, K Amano, M Kinoshita The Journal of chemical physics 131 (20), 2009 | 49 | 2009 |
| Optimized hydrogen mass repartitioning scheme combined with accurate temperature/pressure evaluations for thermodynamic and kinetic properties of biological systems J Jung, K Kasahara, C Kobayashi, H Oshima, T Mori, Y Sugita Journal of Chemical Theory and Computation 17 (8), 5312-5321, 2021 | 47 | 2021 |
| Prediction of protein–ligand binding pose and affinity using the gREST+ FEP method H Oshima, S Re, Y Sugita Journal of Chemical Information and Modeling 60 (11), 5382-5394, 2020 | 43 | 2020 |
| Structural stability of proteins in aqueous and nonpolar environments S Yasuda, H Oshima, M Kinoshita The Journal of chemical physics 137 (13), 2012 | 38 | 2012 |
| Use of multistate Bennett acceptance ratio method for free-energy calculations from enhanced sampling and free-energy perturbation Y Matsunaga, M Kamiya, H Oshima, J Jung, S Ito, Y Sugita Biophysical Reviews 14 (6), 1503-1512, 2022 | 33 | 2022 |
| Reduced efficacy of a Src kinase inhibitor in crowded protein solution K Kasahara, S Re, G Nawrocki, H Oshima, C Mishima-Tsumagari, ... Nature communications 12 (1), 4099, 2021 | 31 | 2021 |
| De novo prediction of binders and nonbinders for T4 lysozyme by gREST simulations A Niitsu, S Re, H Oshima, M Kamiya, Y Sugita Journal of Chemical Information and Modeling 59 (9), 3879-3888, 2019 | 31 | 2019 |
| Storage capacity and retrieval time of small-world neural networks H Oshima, T Odagaki Physical Review E—Statistical, Nonlinear, and Soft Matter Physics 76 (3 …, 2007 | 31 | 2007 |
| Replica-exchange methods for biomolecular simulations Y Sugita, M Kamiya, H Oshima, S Re Biomolecular Simulations: Methods and Protocols, 155-177, 2019 | 29 | 2019 |
| Free‐energy function for discriminating the native fold of a protein from misfolded decoys S Yasuda, T Yoshidome, Y Harano, R Roth, H Oshima, K Oda, Y Sugita, ... Proteins: Structure, Function, and Bioinformatics 79 (7), 2161-2171, 2011 | 29 | 2011 |
| GENESIS 2.1: High-performance molecular dynamics software for enhanced sampling and free-energy calculations for atomistic, coarse-grained, and quantum mechanics/molecular … J Jung, K Yagi, C Tan, H Oshima, T Mori, I Yu, Y Matsunaga, C Kobayashi, ... The Journal of Physical Chemistry B 128 (25), 6028-6048, 2024 | 28 | 2024 |
| Water based on a molecular model behaves like a hard-sphere solvent for a nonpolar solute when the reference interaction site model and related theories are employed T Hayashi, H Oshima, Y Harano, M Kinoshita Journal of Physics: Condensed Matter 28 (34), 344003, 2016 | 25 | 2016 |
| Subway networks in cities KH Chang, K Kim, H Oshima, SM Yoon Journal of the Korean Physical Society 48 (9), 143, 2006 | 25 | 2006 |
Yuji SugitaRIKENVerified email at riken.go.jp
