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Population Shift Mechanism for Partial Agonism of AMPA Receptor.
H. Oshima1, S. Re, M. Sakakura, H. Takahashi, Y. Sugita.
Biophysical Journal, 116, 57-68 (2019).
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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, and M. Kinoshita.
J. Phys.: Condens. Matter, 28, 344003 (2016).
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Statistical Thermodynamics for Actin-Myosin Binding: The Crucial Importance of Hydration Effects.
H. Oshima, T. Hayashi, and M. Kinoshita.
Biophys. J., 110, 2496-2506 (2016).
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A highly efficient hybrid method for calculating the hydration free energy of a protein.
H. Oshima and M. Kinoshita.
J. Comput. Chem., 37, 712-723 (2016).
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Mechanism of One-to-Many Molecular Recognition Accompanying Target-Dependent Structure Formation: For the Tumor Suppressor p53 Protein as an Example.
T. Hayashi, H. Oshima, S. Yasuda, and M. Kinoshita.
J. Phys. Chem. B, 119, 14120-14129 (2015).
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On the physics of thermal-stability changes upon mutations of a protein.
S. Murakami, H. Oshima, T. Hayashi, and M. Kinoshita.
J. Chem. Phys., 143, 125102 (2015).
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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 and M. Kinoshita.
J. Chem. Phys., 142, 145103 (2015).
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Statistical Thermodynamics for Functionally Rotating Mechanism of the Multidrug Efflux Transporter AcrB.
H. Mishima, H. Oshima, S. Yasuda, and M. Kinoshita.
J. Phys. Chem. B, 119, 3423-3433 (2015).
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Changes in hydrophobic and hydrophilic hydration properties caused by raising the pressure or by lowering the temperature.
M. Kinoshita and H. Oshima.
Chem. Phys. Lett., 610-611, 1-7 (2014).
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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, and M. Kinoshita.
Nucleic Acids Res., 42, 6861-6875 (2014).
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Entropic release of a big sphere from a cylindrical vessel.
H. Mishima, H. Oshima, S. Yasuda, K.-I. Amano, and M. Kinoshita.
Chem. Phys. Lett., 561-562, 159-165 (2013).
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Effects of sugars on the thermal stability of a protein.
H. Oshima and M. Kinoshita.
J. Chem. Phys., 138, 245101 (2013).
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On the physics of multidrug efflux through a biomolecular complex.
H. Mishima, H. Oshima, S. Yasuda, K.-I. Amano, and M. Kinoshita.
J. Chem. Phys., 139, 205102 (2013).
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Structural stability of proteins in aqueous and nonpolar environments.
S. Yasuda, H. Oshima, and M. Kinoshita.
J. Chem. Phys., 137, 135103 (2012).
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Characterization of Experimentally Determined Native-Structure Models of a Protein Using Energetic and Entropic Components of Free-Energy Function.
H. Mishima, S. Yasuda, T. Yoshidome, H. Oshima, Y. Harano, M. Ikeguchi, and M. Kinoshita.
J. Phys. Chem. B, 116, 7776-7786 (2012).
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Boundary Perturbation Analysis of Complex Networks.
H. Oshima and T. Odagaki.
J. Phys. Soc. Japan, 81, 124009 (2012).
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Finite Memory Walk and Its Application to Small-World Network.
H. Oshima and T. Odagaki.
J. Phys. Soc. Japan, 81, 074004 (2012).
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An efficient method for analyzing conformational properties of a polymer in solvent.
K.-I. Amano, H. Oshima, and M. Kinoshita.
Chem. Phys. Lett., 504, 7-12 (2011).
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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, M.Ikeguchi, and M. Kinoshita.
Proteins, 79, 2161-2171 (2011).
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Crucial importance of the water-entropy effect in predicting hot spots in protein-protein complexes.
H. Oshima, S. Yasuda, T. Yoshidome, M. Ikeguchi, and M. Kinoshita.
Phys. Chem. Chem. Phys., 13, 16236-16246 (2011).
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Potential of mean force between a large solute and a biomolecular complex: A model analysis on protein flux through chaperonin system.
K.-I. Amano, H. Oshima, and M. Kinoshita.
J. Chem. Phys., 135, 185101 (2011).
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Effects of network structure on associative memory.
H. Oshima and T. Odagaki.
Modelling Perception with Artificial Neural Networks edited by C. R. Tosh and G. D. Ruxton, 134-148 (2010).
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Effects of side-chain packing on the formation of secondary structures in protein folding.
S. Yasuda, T. Yoshidome, H. Oshima, R. Kodama, Y. Harano, and M. Kinoshita.
J. Chem. Phys., 132, 065105 (2010).
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A theoretical analysis on characteristics of protein structures induced by cold denaturation.
H. Oshima, T. Yoshidome, K.-I. Amano, and M. Kinoshita.
J. Chem. Phys., 131, 205102 (2009).
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Storage capacity and retrieval time of small-world neural networks.
H. Oshima and T. Odagaki.
Phys. Rev. E, 76, 036114 (2007).
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Subway networks in cities.
K. H. Chang, K. Kim, H. Oshima, and S.-M. Yoon.
J. Korean Phys. Soc., 48 (SUPPL. 2), S143-S145 (2006).
