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1

An efficient method for analyzing conformational properties of a polymer in solvent

Ken-ich Amano, Hiraku Oshima, Masahiro Kinoshita

Journal:

Chemical Physics Letters

Year:

2011

Language:

english

File:

PDF, 359 KB

english, 2011

2

Corrigendum to: ‘An efficient method for analyzing conformational properties of a polymer in solvent’ [Chem. Phys. Lett. 504 (2011) 7–12]

Ken-ichi Amano, Hiraku Oshima, Masahiro Kinoshita

Journal:

Chemical Physics Letters

Year:

2011

Language:

english

File:

PDF, 120 KB

english, 2011

3

Free-energy function for discriminating the native fold of a protein from misfolded decoys

Satoshi Yasuda, Takashi Yoshidome, Yuichi Harano, Roland Roth, Hiraku Oshima, Koji Oda, Yuji Sugita, Mitsunori Ikeguchi, Masahiro Kinoshita

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

2011

Language:

english

File:

PDF, 688 KB

english, 2011

4

Characterization of Experimentally Determined Native-Structure Models of a Protein Using Energetic and Entropic Components of Free-Energy Function

Mishima, Hirokazu, Yasuda, Satoshi, Yoshidome, Takashi, Oshima, Hiraku, Harano, Yuichi, Ikeguchi, Mitsunori, Kinoshita, Masahiro

Journal:

Journal of Physical Chemistry B

Year:

2012

Language:

english

File:

PDF, 1.49 MB

english, 2012

5

Mouse gastric tumor models with prostaglandin E2pathway activation show similar gene expression profiles to intestinal-type human gastric cancer

Hiraku Itadani, Hiroko Oshima, Masanobu Oshima, Hidehito Kotani

Journal:

Year:

2009

Language:

english

File:

PDF, 333 KB

english, 2009

6

Crucial importance of the water-entropy effect in predicting hot spots in protein–protein complexes

Oshima, Hiraku, Yasuda, Satoshi, Yoshidome, Takashi, Ikeguchi, Mitsunori, Kinoshita, Masahiro

Journal:

Physical Chemistry Chemical Physics

Year:

2011

Language:

english

File:

PDF, 2.00 MB

english, 2011

7

Induction and Down-regulation of Sox17 and Its Possible Roles During the Course of Gastrointestinal Tumorigenesis

Yu–Chen Du, Hiroko Oshima, Keisuke Oguma, Takanori Kitamura, Hiraku Itadani, Takashi Fujimura, Ying–Shi Piao, Tanihiro Yoshimoto, Toshinari Minamoto, Hidehito Kotani, Makoto M. Taketo, Masanobu Oshima

Journal:

Gastroenterology

Year:

2009

Language:

english

File:

PDF, 2.88 MB

english, 2009

8

Effects of sugars on the thermal stability of a protein

Oshima, Hiraku, Kinoshita, Masahiro

Journal:

The Journal of Chemical Physics

Year:

2013

Language:

english

File:

PDF, 714 KB

english, 2013

9

Statistical Thermodynamics for Binding of an RNA Aptamer and a Partial Peptide of a Prion Protein

Hayashi, Tomohiko, Oshima, Hiraku, Mashima, Tsukasa, Nagata, Takashi, Katahira, Masato, Kinoshita, Masahiro

Journal:

Biophysical Journal

Year:

2014

Language:

english

File:

PDF, 41 KB

english, 2014

10

Crucial Importance of Protein-Solvent Many-Body Correlation for Solvent-Entropy Effect in Structural Stability of a Protein

Oshima, Hiraku, Kinoshita, Masahiro

Journal:

Biophysical Journal

Year:

2014

Language:

english

File:

PDF, 62 KB

english, 2014

11

Effects of Sugars on the Thermal Stability of a Protein

Oshima, Hiraku, Kinoshita, Masahiro

Journal:

Biophysical Journal

Year:

2013

Language:

english

File:

PDF, 38 KB

english, 2013

12

Entropic release of a big sphere from a cylindrical vessel

Mishima, Hirokazu, Oshima, Hiraku, Yasuda, Satoshi, Amano, Ken-ichi, Kinoshita, Masahiro

Journal:

Chemical Physics Letters

Year:

2013

Language:

english

File:

PDF, 849 KB

english, 2013

13

Physics of Multidrug Efflux through a Biomolecular Complex

Mishima, Hirokazu, Oshima, Hiraku, Yasuda, Satoshi, Amano, Ken-ichi, Kinoshita, Masahiro

Journal:

Biophysical Journal

Year:

2014

Language:

english

File:

PDF, 43 KB

english, 2014

14

Storage capacity and retrieval time of small-world neural networks

Oshima, Hiraku, Odagaki, Takashi

Journal:

Physical Review E

Year:

2007

Language:

english

File:

PDF, 189 KB

english, 2007

15

Changes in hydrophobic and hydrophilic hydration properties caused by raising the pressure or by lowering the temperature

Kinoshita, Masahiro, Oshima, Hiraku

Journal:

Chemical Physics Letters

Year:

2014

Language:

english

File:

PDF, 1.04 MB

english, 2014

16

Structural stability of proteins in aqueous and nonpolar environments

Yasuda, Satoshi, Oshima, Hiraku, Kinoshita, Masahiro

Journal:

The Journal of Chemical Physics

Year:

2012

Language:

english

File:

PDF, 2.85 MB

english, 2012

17

Effects of side-chain packing on the formation of secondary structures in protein folding

Yasuda, Satoshi, Yoshidome, Takashi, Oshima, Hiraku, Kodama, Ryota, Harano, Yuichi, Kinoshita, Masahiro

Journal:

The Journal of Chemical Physics

Year:

2010

Language:

english

File:

PDF, 2.11 MB

english, 2010

18

On the physics of multidrug efflux through a biomolecular complex

Mishima, Hirokazu, Oshima, Hiraku, Yasuda, Satoshi, Amano, Ken-ichi, Kinoshita, Masahiro

Journal:

The Journal of Chemical Physics

Year:

2013

Language:

english

File:

PDF, 3.38 MB

english, 2013

19

A theoretical analysis on characteristics of protein structures induced by cold denaturation

Oshima, Hiraku, Yoshidome, Takashi, Amano, Ken-ichi, Kinoshita, Masahiro

Journal:

The Journal of Chemical Physics

Year:

2009

Language:

english

File:

PDF, 1.16 MB

english, 2009

20

Potential of mean force between a large solute and a biomolecular complex: A model analysis on protein flux through chaperonin system

Amano, Ken-ich, Oshima, Hiraku, Kinoshita, Masahiro

Journal:

The Journal of Chemical Physics

Year:

2011

Language:

english

File:

PDF, 2.72 MB

english, 2011

21

Statistical Thermodynamics for Functionally Rotating Mechanism of the Multidrug Efflux Transporter AcrB

Mishima, Hirokazu, Oshima, Hiraku, Yasuda, Satoshi, Kinoshita, Masahiro

Journal:

Journal of Physical Chemistry B

Year:

2015

Language:

english

File:

PDF, 502 KB

english, 2015

22

Essential roles of protein-solvent many-body correlation in solvent-entropy effect on protein folding and denaturation: Comparison between hard-sphere solvent and water

Oshima, Hiraku, Kinoshita, Masahiro

Journal:

The Journal of Chemical Physics

Year:

2015

Language:

english

File:

PDF, 1.33 MB

english, 2015

23

Mechanism of One-to-Many Molecular Recognition Accompanying Target-Dependent Structure Formation: For the Tumor Suppressor p53 Protein as an Example

Hayashi, Tomohiko, Oshima, Hiraku, Yasuda, Satoshi, Kinoshita, Masahiro

Journal:

Journal of Physical Chemistry B

Year:

2015

Language:

english

File:

PDF, 1.32 MB

english, 2015

24

Theoretical Prediction of Thermal-Stability Changes upon Mutations of a Protein

Murakami, Shota, Oshima, Hiraku, Hayashi, Tomohiko, Kinoshita, Masahiro

Journal:

Biophysical Journal

Year:

2015

Language:

english

File:

PDF, 40 KB

english, 2015

25

Statistical Thermodynamics of One-To-Many Molecular Recognition Accompanied by Partner-Dependent Folding: In the Case of a Tumor Suppressor Protein p53

Hayashi, Tomohiko, Oshima, Hiraku, Yasuda, Satoshi, Kinoshita, Masahiro

Journal:

Biophysical Journal

Year:

2015

Language:

english

File:

PDF, 42 KB

english, 2015

26

Essential Roles of Water in Actin-Myosin Binding

Oshima, Hiraku, Hayashi, Tomohiko, Kinoshita, Masahiro

Journal:

Biophysical Journal

Year:

2016

Language:

english

File:

PDF, 39 KB

english, 2016

27

Physical Picture for Functionally Rotating Mechanism of the Multidrug Efflux Transporter AcrB

Mishima, Hirokazu, Oshima, Hiraku, Yasuda, Satoshi, Kinoshita, Masahiro

Journal:

Biophysical Journal

Year:

2015

Language:

english

File:

PDF, 39 KB

english, 2015

28

Statistical Thermodynamics for Actin-Myosin Binding: The Crucial Importance of Hydration Effects

Oshima, Hiraku, Hayashi, Tomohiko, Kinoshita, Masahiro

Journal:

Biophysical Journal

Year:

2016

Language:

english

File:

PDF, 893 KB

english, 2016

29

A highly efficient hybrid method for calculating the hydration free energy of a protein

Oshima, Hiraku, Kinoshita, Masahiro

Journal:

Journal of Computational Chemistry

Year:

2016

Language:

english

File:

PDF, 803 KB

english, 2016

30

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

Hayashi, Tomohiko, Oshima, Hiraku, Harano, Yuichi, Kinoshita, Masahiro

Journal:

Journal of Physics Condensed Matter

Year:

2016

Language:

english

File:

PDF, 1.24 MB

english, 2016

31

Finite Memory Walk and Its Application to Small-World Network

Oshima, Hiraku, Odagaki, Takashi

Journal:

Journal of the Physical Society of Japan

Year:

2012

Language:

english

File:

PDF, 621 KB

english, 2012

32

Production of novel bispyrone metabolites in the cellular slime mold Dictyostelium giganteum induced by zinc(II) ion

Nguyen, Van Hai, Kikuchi, Haruhisa, Sasaki, Hiraku, Iizumi, Kyoichi, Kubohara, Yuzuru, Oshima, Yoshiteru

Journal:

Year:

2017

Language:

english

File:

PDF, 764 KB

english, 2017

33

On the physics of thermal-stability changes upon mutations of a protein

Murakami, Shota, Oshima, Hiraku, Hayashi, Tomohiko, Kinoshita, Masahiro

Journal:

The Journal of Chemical Physics

Year:

2015

Language:

english

File:

PDF, 3.64 MB

english, 2015

34

Boundary Perturbation Analysis of Complex Networks

Oshima, Hiraku, Odagaki, Takashi

Journal:

Journal of the Physical Society of Japan

Year:

2012

Language:

english

File:

PDF, 890 KB

english, 2012

35

Generation of branching ureteric bud tissues from human pluripotent stem cells

Mae, Shin-Ichi, Ryosaka, Makoto, Toyoda, Taro, Matsuse, Kyoko, Oshima, Yoichi, Tsujimoto, Hiraku, Okumura, Shiori, Shibasaki, Aya, Osafune, Kenji

Journal:

Biochemical and Biophysical Research Communications

Year:

2017

Language:

english

File:

PDF, 3.76 MB

english, 2017

36

1P-045 A Theoretical Analysis on Characteristics of Protein Structures Induced by Cold Denaturation(Protein:Property, The 47th Annual Meeting of the Biophysical Society of Japan)

Oshima, Hiraku, Yoshidome, Takashi, Amano, Ken-ichi, Kinoshita, Masahiro

Journal:

Seibutsu Butsuri

Year:

2009

Language:

english

File:

PDF, 234 KB

english, 2009

37

1P062 Theoretical Prediction of Hot Spots in Protein-Protein Complexes(Protein:Property,The 48th Annual Meeting of the Biophysical Society of Japan)

Oshima, Hiraku, Yasuda, Satoshi, Yoshidome, Takashi, Ikeguchi, Mitsunori, Kinoshita, Masahiro

Journal:

Seibutsu Butsuri

Year:

2010

Language:

english

File:

PDF, 232 KB

english, 2010

38

1PT154 Structural stability of a protein in aqueous and nonaqueous environments(The 50th Annual Meeting of the Biophysical Society of Japan)

Yasuda, Satoshi, Oshima, Hiraku, Kinoshita, Masahiro

Journal:

Seibutsu Butsuri

Year:

2012

Language:

english

File:

PDF, 217 KB

english, 2012

39

3P114 Statistical Thermodynamics for Binding of an RNA Aptamer and a Partial Peptide of a Prion Protein(04. Nucleic acid binding proteins,Poster)

Hayashi, Tomohiko, Oshima, Hiraku, Mashima, Tsukasa, Nagata, Takashi, Katahira, Masato, Kinoshita, Masahiro

Journal:

Seibutsu Butsuri

Year:

2013

Language:

english

File:

PDF, 695 KB

english, 2013

40

3P058 Solvent-Entropy Effect in Structural Stability of a Protein : Crucial Importance of Protein-Solvent Many-Body Correlation(01A. Protein: Structure,Poster)

Oshima, Hiraku, Murakami, Shota, Kinoshita, Masahiro

Journal:

Seibutsu Butsuri

Year:

2013

Language:

english

File:

PDF, 1.04 MB

english, 2013

41

2P004 Statistical thermodynamics of one-to-many molecular recognition accompanied by partner-dependent folding : in the case of p53 protein(01A. Protein:Structure,Poster,The 52nd Annual Meeting of the Biophysical Society of Japan(BSJ2014))

Hayashi, Tomohiko, Oshima, Hiraku, Yasuda, Satoshi, Kinoshita, Masahiro

Journal:

Seibutsu Butsuri

Year:

2014

Language:

english

File:

PDF, 694 KB

english, 2014

42

3P057 Theoretical Prediction of Thermal-Stability Changes upon Mutations of a Protein(01A. Protein: Structure,Poster)

Murakami, Shota, Oshima, Hiraku, Hayashi, Tomohiko, Kinoshita, Masahiro

Journal:

Seibutsu Butsuri

Year:

2013

Language:

english

File:

PDF, 1.04 MB

english, 2013

43

3P057 Theoretical Prediction of Thermal-Stability Changes upon Mutations of a Protein(01C. Protein: Property,Poster,The 52nd Annual Meeting of the Biophysical Society of Japan(BSJ2014))

Murakami, Shota, Oshima, Hiraku, Hayashi, Tomohiko, Kinoshita, Masahiro

Journal:

Seibutsu Butsuri

Year:

2014

Language:

english

File:

PDF, 1.01 MB

english, 2014

44

1H1436 Crucial Importance of Water-Entropy Effect for Hot Spots in Protein-Protein Complexes(Protein: Property 2,The 49th Annual Meeting of the Biophysical Society of Japan)

Oshima, Hiraku, Yasuda, Satoshi, Yoshidome, Takashi, Ikeguchi, Mitsunori, Kinoshita, Masahiro

Journal:

Seibutsu Butsuri

Year:

2011

Language:

english

File:

PDF, 225 KB

english, 2011

45

3P109 Theoretical Enhancement of Structural Stability of a Membrane Protein for X-ray Crystallography(03. Membrane proteins,Poster)

Yasuda, Satoshi, Oshima, Hiraku, Murata, Takeshi, Kinoshita, Masahiro

Journal:

Seibutsu Butsuri

Year:

2013

Language:

english

File:

PDF, 695 KB

english, 2013

46

3P024 Physical Picture for Mechanism of Conformational Rotation of Multidrug Transporter AcrB(01B. Protein: Structure & Function,Poster,The 52nd Annual Meeting of the Biophysical Society of Japan(BSJ2014))

Mishima, Hirokazu, Oshima, Hiraku, Yasuda, Satoshi, Kinoshita, Masahiro

Journal:

Seibutsu Butsuri

Year:

2014

Language:

english

File:

PDF, 729 KB

english, 2014

47

3PT116 Entropic release of a big sphere from a cylindrical vessel(The 50th Annual Meeting of the Biophysical Society of Japan)

Mishima, Hirokazu, Oshima, Hiraku, Yasuda, Satoshi, Amano, Ken-ichi, Kinoshita, Masahiro

Journal:

Seibutsu Butsuri

Year:

2012

Language:

english

File:

PDF, 215 KB

english, 2012

48

3P108 On the Physics of Multidrug Efflux through a Biomolecular Complex(03. Membrane proteins,Poster)

Mishima, Hirokazu, Oshima, Hiraku, Yasuda, Satoshi, Amano, Ken-ichi, Kinoshita, Masahiro

Journal:

Seibutsu Butsuri

Year:

2013

Language:

english

File:

PDF, 694 KB

english, 2013

49

1PT137 Effects of sugars on the thermal stability of proteins(The 50th Annual Meeting of the Biophysical Society of Japan)

Oshima, Hiraku, Amano, Ken-ichi, Kinoshita, Masahiro

Journal:

Seibutsu Butsuri

Year:

2012

Language:

english

File:

PDF, 210 KB

english, 2012

50

Population Shift Mechanism for Partial Agonism of AMPA Receptor

Oshima, Hiraku, Re, Suyong, Sakakura, Masayoshi, Takahashi, Hideo, Sugita, Yuji

Journal:

Biophysical Journal

Year:

2019

Language:

english

File:

PDF, 3.52 MB

english, 2019