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Hiraku Oshima
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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
852014
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
682019
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
672020
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
602015
Effects of sugars on the thermal stability of a protein
H Oshima, M Kinoshita
Biophysical Journal 104 (2), 563a, 2013
562013
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
492009
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
482010
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
442019
Structural stability of proteins in aqueous and nonpolar environments
S Yasuda, H Oshima, M Kinoshita
The Journal of chemical physics 137 (13), 2012
342012
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
322020
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
322007
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
292011
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
262019
Replica-exchange methods for biomolecular simulations
Y Sugita, M Kamiya, H Oshima, S Re
Biomolecular Simulations: Methods and Protocols, 155-177, 2019
262019
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
252021
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
242021
Crucial importance of the water-entropy effect in predicting hot spots in protein–protein complexes
H Oshima, S Yasuda, T Yoshidome, M Ikeguchi, M Kinoshita
Physical Chemistry Chemical Physics 13 (36), 16236-16246, 2011
242011
Subway networks in cities
KH Chang, K Kim, H Oshima, SM Yoon
Journal of the Korean Physical Society 48 (9), 143, 2006
242006
Potential of mean force between a large solute and a biomolecular complex: a model analysis on protein flux through chaperonin system
K Amano, H Oshima, M Kinoshita
The Journal of chemical physics 135 (18), 2011
232011
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
222016
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Articles 1–20