Publications

論文

1. Y. Matsunaga, M. Kamiya, H. Oshima, J. Jung, S. Ito, Y, Sugita, “Use of multistate Bennett acceptance ratio method for free-energy calculations from enhanced sampling and free-energy perturbation”, Biophys. Rev. 14, 1503–1512 (2022).

2. D. Matsubara, K. Kasahara, H. M. Dokainish, H. Oshima, Y. Sugita, “Modified Protein-Water Interactions in CHARMM36m for Thermodynamics and Kinetics of Proteins in Dilute and Crowded Solutions”, Molecules 27, 5726 (2022)

3. H. Oshima and Y. Sugita, “Modified Hamiltonian in FEP Calculations for Reducing the Computational Cost of Electrostatic Interactions”, J. Chem. Inf. Model. 62, 2846-2856 (2022)

4. J. Jung, K. Kasahara, C. Kobayashi, H. Oshima, T. Mori, Y. Sugita, “Optimized hydrogen mass repartitioning scheme combined with accurate temperature/pressure evaluations for thermodynamic and kinetic properties of biological systems”, J. Chem. Theory Comput. 17, 5312-5321 (2021)

5. K. Kasahara, S. Re, G. Nawrocki, H. Oshima, C. Mishima-Tsumagari, Y. Miyata-Yabuki, M. Kukimoto-Niino, I. Yu, M. Shirouzu, M. Feig, Y. Sugita, “Reduced efficacy of a Src kinase inhibitor in crowded protein solution”, Nat. Comm., 12, 4099 (2021)

6. W. Ren, H. Dokainish, A. Shinobu, H. Oshima, Y. Sugita, "Unraveling the coupling between conformational changes and ligand-binding in ribose binding protein using multi-scale molecular dynamics and free-energy calculations", J. Phys. Chem. B, 125, 2898-2909 (2021)

7. S. Kim, H. Oshima, H. Zhang, N. R. Kern, S. Re, J. Lee, B. Roux, Y. Sugita, W. Jiang, W. Im, “CHARMM-GUI Free Energy Calculator for Absolute and Relative Ligand Solvation and Binding Free Energy Simulations”, J. Chem. Theory Comput. 16, 7207-7218 (2020)

8. H. Oshima, S. Re, Y. Sugita, “Prediction of Protein–Ligand Binding Pose and Affinity Using the gREST+FEP Method”, J. Chem. Inf. Model. 60, 5382-5394 (2020)

9. D. Fujinami, H. Motomura, H. Oshima, Abdullah-Al Mahin, K. M. Elsayed, T. Zendo, Y. Sugita, K. Sonomoto, D. Kohda, “Mosaic Cooperativity in Slow Polypeptide Topological Isomerization Revealed by Residue-Specific NMR Thermodynamic Analysis.”, J. Phys. Chem. Lett. 11, 1934-1939 (2020)

10. H. Oshima, S. Re, and Y. Sugita, “Replica-exchange umbrella sampling combined with Gaussian accelerated molecular dynamics for free-energy calculation of biomolecules.”, J. Chem. Theory Comput. 15, 5199-5208 (2019)

11. M. Sakakura, Y. Ohkubo, H. Oshima, S. Re, M. Ito, Y. Sugita, and H. Takahashi, “Structural mechanisms underlying activity changes in an AMPA-type glutamate receptor induced by substitutions in its ligand-binding domain.”, Structure 27, 1698-1709 (2019)

12. A. Niitsu, S. Re, H. Oshima, M. Kamiya, and Y. Sugita, “De Novo Prediction of Binders and Nonbinders for T4 Lysozyme by gREST Simulations.”, J. Chem. Inf. Model. 59, 3879-3888 (2019)

13. S. Re, H. Oshima, K. Kasahara, M. Kamiya, and Y. Sugita, “Encounter complexes and hidden poses of kinase-inhibitor binding on the free-energy landscape.”, Proc. Natl. Acad. Sci. USA 116, 18404-18409 (2019)

14. H. Oshima, S. Re, M. Sakakura, H. Takahashi, and Y. Sugita, “Population Shift Mechanism for Partial Agonism of AMPA Receptor”, Biophys. J. 116, 57-68 (2019)

15. T. Hayashi, H. Oshima, Y. Harano, and M. Kinoshita, “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”, J. Phys.: Condens. Matter 28, 344003 (2016)

16. H. Oshima, T. Hayashi, and M. Kinoshita, “Statistical Thermodynamics for Actin-Myosin Binding: The Crucial Importance of Hydration Effects”, Biophysical Journal 110, 2496-2506 (2016)

17. H. Oshima and M. Kinoshita, “A highly efficient hybrid method for calculating the hydration free energy of a protein”, Journal of Computational Chemistry 37, 712-723 (2016)

18. T. Hayashi, H. Oshima, S. Yasuda, and M. Kinoshita, “Mechanism of One-to-many Molecular Recognition Accompanying Target-dependent Structure Formation: For the Tumor Suppressor p53 Protein as an Example”, Journal of Physical Chemistry B 119, 14120–14129 (2015)

19. S. Murakami, H. Oshima, T. Hayashi, and M. Kinoshita, “On the physics of thermal-stability changes upon mutations of a protein”, Journal of Chemical Physics 143, 125102 (2015)

20. H. Oshima and M. Kinoshita, “Essential roles of protein-solvent many-body correlation in solvent-entropy effect on protein folding and denaturation: Comparison between hard-sphere solvent and water”, Journal of Chemical Physics 142, 145103 (2015).

21. H. Mishima, H. Oshima, S. Yasuda, and M. Kinoshita, “Statistical Thermodynamics for Functionally Rotating Mechanism of the Multidrug Efflux Transporter AcrB”, Journal of Physical Chemistry B 119, 3423-3433 (2015).

22. M. Kinoshita and H. Oshima, “Changes in hydrophobic and hydrophilic hydration properties caused by raising the pressure or by lowering the temperature”, Chemical Physics Letters 610-611, 1-7, (2014).

23. T. Hayashi, H. Oshima, T. Mashima, T. Nagata, M. Katahira, and M. Kinoshita, “Binding of an RNA aptamer and a partial peptide of a prion protein: crucial importance of water entropy in molecular recognition”, Nucleic Acids Research 42, 6861-6875 (2014).

24. H. Mishima, H. Oshima, S. Yasuda, K.-I. Amano, and M. Kinoshita, “Entropic release of a big sphere from a cylindrical vessel”, Chemical Physics Letters 561-562, 159–165 (2013).

25. H. Oshima and M. Kinoshita, “Effects of sugars on the thermal stability of a protein”, Journal of Chemical Physics 138, 245101 (2013)

26. H. Mishima, H. Oshima, S. Yasuda, K.-I. Amano, and M. Kinoshita, “On the physics of multidrug efflux through a biomolecular complex”, Journal of Chemical Physics 139, 205102 (2013).

27. S. Yasuda, H. Oshima, and M. Kinoshita, “Structural stability of proteins in aqueous and nonpolar environments”, Journal of Chemical Physics 137, 135103 (2012).

28. H. Mishima, S. Yasuda, T. Yoshidome, H. Oshima, Y. Harano, M. Ikeguchi, and M. Kinoshita, “Characterization of Experimentally Determined Native-Structure Models of a Protein Using Energetic and Entropic Components of Free-Energy Function”, Journal of Physical Chemistry B 116, 7776–7786 (2012).

29. H. Oshima and T. Odagaki, “Boundary Perturbation Analysis of Complex Networks”, Journal of the Physical Society of Japan 81, 124009 (2012).

30. H. Oshima and T. Odagaki, “Finite Memory Walk and Its Application to Small-World Network”, Journal of the Physical Society of Japan 81, 074004 (2012).

31. K.-I. Amano, H. Oshima, and M. Kinoshita, "An efficient method for analyzing conformational properties of a polymer in solvent", Chemical Physics Letters 504, 7-12 (2011).

32. S. Yasuda, T. Yoshidome, Y. Harano, R. Roth, H. Oshima, K. Oda, Y. Sugita, M.Ikeguchi, and M. Kinoshita, "Free-energy function for discriminating the native fold of a protein from misfolded decoys", Proteins 79, 2161-2171 (2011).

33. H. Oshima, S. Yasuda, T. Yoshidome, M. Ikeguchi, and M. Kinoshita, "Crucial importance of the water-entropy effect in predicting hot spots in protein-protein complexes", Physical Chemistry Chemical Physics 13, 16236-16246 (2011).

34. K.-I. Amano, H. Oshima, and M. Kinoshita, "Potential of mean force between a large solute and a biomolecular complex: A model analysis on protein flux through chaperonin system", Journal of Chemical Physics 135, 185101 (2011).

35. S. Yasuda, T. Yoshidome, H. Oshima, R. Kodama, Y. Harano, and M. Kinoshita, "Effects of side-chain packing on the formation of secondary structures in protein folding", Journal of Chemical Physics 132, 065105 (2010).

36. H. Oshima, T. Yoshidome, K.-I. Amano, and M. Kinoshita, "A theoretical analysis on characteristics of protein structures induced by cold denaturation", Journal of Chemical Physics 131, 205102 (2009).

37. H. Oshima and T. Odagaki, "Storage capacity and retrieval time of small-world neural networks", Physical Review E 76, 036114 (2007).

38. K.H. Chang, K. Kim, H. Oshima, and S.-M. Yoon, "Subway networks in cities", Journal of the Korean Physical Society 48 (SUPPL. 2), S143-S145 (2006)

総説・解説

1. 尾嶋拓, “GaREUS 法を用いた自由エネルギー地形の計算”, 蛋白質科学会アーカイブ, 14, e105 (2021)

2. 尾嶋拓，李秀栄，新津藍，杉田有治, “分子動力学ソフトウェアGENESISを用いたタンパク質―リガンド結合の自由エネルギー計算”, 日本シミュレーション学会誌“シミュレーション”, Vol. 40, pp. 22–28 (2021)

著書

1. Y. Sugita, M. Kamiya, H. Oshima, and S. Re, “Replica-Exchange Methods for Biomolecular Simulations”, In: M. Bonomi, C. Camilloni (eds) Biomolecular Simulations, pp. 155-177, Humana, New York, NY (2019)

2. H. Oshima and T. Odagaki, "Effects of network structure on associative memory", In: C. R. Tosh and G. D. Ruxton (eds) Modelling Perception with Artificial Neural Networks, pp. 134-148, Cambridge University Press (2010).