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1

Multidimensional replica-exchange method for free-energy calculations

Sugita, Yuji, Kitao, Akio, Okamoto, Yuko

Journal:

The Journal of Chemical Physics

Year:

2000

Language:

english

File:

PDF, 361 KB

english, 2000

2

Multiple Markov transition matrix method: Obtaining the stationary probability distribution from multiple simulations

Shun Sakuraba, Akio Kitao

Journal:

Journal of Computational Chemistry

Year:

2009

Language:

english

File:

PDF, 382 KB

english, 2009

3

Origins of biological function in DNA and RNA hairpin loop motifs from replica exchange molecular dynamics simulation

Swadling, Jacob B., Ishii, Kunihiko, Tahara, Tahei, Kitao, Akio

Journal:

Physical Chemistry Chemical Physics

Year:

2018

Language:

english

File:

PDF, 4.04 MB

english, 2018

4

Model-free methods of analyzing domain motions in proteins from simulation: A comparison of normal mode analysis and molecular dynamics simulation of lysozyme

Steven Hayward, Akio Kitao, Herman J.C. Berendsen

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

1997

Language:

english

File:

PDF, 185 KB

english, 1997

5

Improved protein free energy calculation by more accurate treatment of nonbonded energy: Application to chymotrypsin inhibitor 2, V57A

Yuji Sugita, Akio Kitao

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

1998

Language:

english

File:

PDF, 347 KB

english, 1998

6

Energy landscape of a native protein: Jumping-among-minima model

Akio Kitao, Steven Hayward, Nobuhiro Go

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

1998

Language:

english

File:

PDF, 285 KB

english, 1998

7

Conformational dynamics of polypeptides and proteins in the dihedral angle space and in the cartesian coordinate space: Normal mode analysis of deca-alanine

Akio Kitao, Nobuhiro Gō

Journal:

Journal of Computational Chemistry

Year:

1991

Language:

english

File:

PDF, 882 KB

english, 1991

8

Amplitudes and directions of internal protein motions from a JAM analysis of 15N relaxation data

Akio Kitao, Gerhard Wagner

Journal:

Magnetic Resonance in Chemistry

Year:

2006

Language:

english

File:

PDF, 2.07 MB

english, 2006

9

The effects of solvent on the conformation and the collective motions of protein: Normal mode analysis and molecular dynamics simulations of melittin in water and in vacuum

Akio Kitao, Fumio Hirata, Nobuhiro Gō

Journal:

Chemical Physics

Year:

1991

Language:

english

File:

PDF, 2.31 MB

english, 1991

10

Comparison of normal mode analyses on a small globular protein in dihedral angle space and Cartesian coordinate space

Akio Kitao, Steven Hayward, Nobuhiro Go

Journal:

Biophysical Chemistry

Year:

1994

Language:

english

File:

PDF, 707 KB

english, 1994

11

Multi-Scale Free Energy Landscape calculation method by combination of coarse-grained and all-atom models

Ryuhei Harada, Akio Kitao

Journal:

Chemical Physics Letters

Year:

2011

Language:

english

File:

PDF, 1.29 MB

english, 2011

12

Mechanical unfolding of bacterial flagellar filament protein by molecular dynamics simulation

Choon-Peng Chng, Akio Kitao

Journal:

Journal of Molecular Graphics and Modelling

Year:

2010

Language:

english

File:

PDF, 528 KB

english, 2010

13

Molecular simulation study to examine the possibility of detecting collective motion in protein by inelastic neutron scattering

Yasumasa Joti, Akio Kitao, Nobuhiro Go

Journal:

Physica B: Condensed Matter

Year:

2004

Language:

english

File:

PDF, 183 KB

english, 2004

14

Harmonic and anharmonic aspects in the dynamics of BPTI: A normal mode analysis and principal component analysis

Steven Hayward, Akio Kitao, Nobuhiro Gō

Journal:

Protein Science

Year:

1994

Language:

english

File:

PDF, 771 KB

english, 1994

15

Harmonicity and anharmonicity in protein dynamics: A normal mode analysis and principal component analysis

Steven Hayward, Akio Kitao, Professor Nobuhiro Gō

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

1995

Language:

english

File:

PDF, 926 KB

english, 1995

16

Molecular dynamics simulation shows large volume fluctuations of proteins

Florence Tama, Osamu Miyashita, Akio Kitao, Nobuhiro Go

Journal:

European Biophysics Journal

Year:

2000

Language:

english

File:

PDF, 300 KB

english, 2000

17

Hydration-coupled protein boson peak measured by incoherent neutron scattering

Hiroshi Nakagawa, Mikio Kataoka, Yasumasa Joti, Akio Kitao, Kaoru Shibata, Atsushi Tokuhisa, Itaru Tsukushi, Nobuhiro Go

Journal:

Physica B: Condensed Matter

Year:

2006

Language:

english

File:

PDF, 147 KB

english, 2006

18

Inhibition of 1,2-Dimethylhydrazine-induced Oxidative DNA Damage by Green Tea Extract in Rat

Masao Inagake, Tetsuro Yamane, Yoshitaka Kitao, Kazuhiko Oya, Hirohiko Matsuraoto, Norikazu Kikuoka, Hirohisa Nakatani, Toshio Takahashi, Hiroshi Nishimura, Akio Iwashiraa

Journal:

Year:

1995

File:

PDF, 393 KB

1995

19

A requirement of FancL and FancD2 monoubiquitination in DNA repair

Sohsuke Seki, Mioko Ohzeki, Akiko Uchida, Seiki Hirano, Nobuko Matsushita, Hiroyuki Kitao, Tsukasa Oda, Takayuki Yamashita, Naoki Kashihara, Akio Tsubahara, Minoru Takata, Masamichi Ishiai

Journal:

Year:

2007

Language:

english

File:

PDF, 396 KB

english, 2007

20

Structure of the cytoplasmic domain of FlhA and implication for flagellar type III protein export

Yumiko Saijo-Hamano, Katsumi Imada, Tohru Minamino, May Kihara, Masafumi Shimada, Akio Kitao, Keiichi Namba

Journal:

Molecular Microbiology

Year:

2010

Language:

english

File:

PDF, 627 KB

english, 2010

21

Structure of the bacterial flagellar hook and implication for the molecular universal joint mechanism

Samatey, Fadel A., Matsunami, Hideyuki, Imada, Katsumi, Nagashima, Shigehiro, Shaikh, Tanvir R., Thomas, Dennis R., Chen, James Z., DeRosier, David J., Kitao, Akio, Namba, Keiichi

Journal:

Year:

2004

Language:

english

File:

PDF, 655 KB

english, 2004

22

Non-Gaussian behavior of elastic incoherent neutron scattering profiles of proteins studied by molecular dynamics simulation

Tokuhisa, Atsushi, Joti, Yasumasa, Nakagawa, Hiroshi, Kitao, Akio, Kataoka, Mikio

Journal:

Physical Review E

Year:

2007

Language:

english

File:

PDF, 699 KB

english, 2007

23

A Collective Motion Description of the 310-/.alpha.-Helix Transition: Implications for a Natural Reaction Coordinate

Basu, Gautam, Kitao, Akio, Hirata, Fumio, Go, Nobuhiro

Journal:

Journal of the American Chemical Society

Year:

1994

Language:

english

File:

PDF, 1.82 MB

english, 1994

24

Erratum to ‘Multi-Scale Free Energy Landscape calculation method by combination of coarse-grained and all-atom models’ [Chem. Phys. Lett. 503 (2011) 145–152]

Ryuhei Harada, Akio Kitao

Journal:

Chemical Physics Letters

Year:

2011

Language:

english

File:

PDF, 129 KB

english, 2011

25

Investigating protein dynamics in collective coordinate space

Akio Kitao, Nobuhiro Go

Journal:

Current Opinion in Structural Biology

Year:

1999

Language:

english

File:

PDF, 738 KB

english, 1999

26

Computational analysis of thermal stability: effect of Ile→Val mutations in human lysozyme

Yuji Sugita, Akio Kitao, Nobuhiro Go

Journal:

Folding and Design

Year:

1998

Language:

english

File:

PDF, 296 KB

english, 1998

27

Effect of Solvent on Collective Motions in Globular Protein

S. Hayward, Akio Kitao, Fumio Hirata, Nobuhiro Gō

Journal:

Journal of Molecular Biology

Year:

1993

File:

PDF, 682 KB

1993

28

Gap compression/extension mechanism of bacterial flagellar hook as the molecular universal joint

Tadaomi Furuta, Fadel A. Samatey, Hideyuki Matsunami, Katsumi Imada, Keiichi Namba, Akio Kitao

Journal:

Journal of Structural Biology

Year:

2007

Language:

english

File:

PDF, 2.33 MB

english, 2007

29

Enhanced resolution of molecular recognition to distinguish structurally similar molecules by different conformational responses of a protein upon ligand binding

Mariko Higuchi, Jumpei Fujii, Yoshiteru Yonetani, Akio Kitao, Nobuhiro Go

Journal:

Journal of Structural Biology

Year:

2011

Language:

english

File:

PDF, 1.45 MB

english, 2011

30

Effects of Water Model and Simulation Box Size on Protein Diffusional Motions

Takemura, Kazuhiro, Kitao, Akio

Journal:

Journal of Physical Chemistry B

Year:

2007

Language:

english

File:

PDF, 89 KB

english, 2007

31

Linear Response of Biomolecules To External Perturbations: Revisit Induce-fit

Yang, Lee Wei, Kitao, Akio, Go, Nobuhiro

Journal:

Biophysical Journal

Year:

2009

Language:

english

File:

PDF, 39 KB

english, 2009

32

Collective Dynamics of Periplasmic Glutamine Binding Protein upon Domain Closure

Loeffler, Hannes H., Kitao, Akio

Journal:

Biophysical Journal

Year:

2009

Language:

english

File:

PDF, 821 KB

english, 2009

33

The Effect of End Constraints on Protein Loop Kinematics

Hayward, Steven, Kitao, Akio

Journal:

Biophysical Journal

Year:

2010

Language:

english

File:

PDF, 1.03 MB

english, 2010

34

Dependence of Protein Stability on the Structure of the Denatured State: Free Energy Calculations of I56V Mutation in Human Lysozyme

Sugita, Yuji, Kitao, Akio

Journal:

Biophysical Journal

Year:

1998

Language:

english

File:

PDF, 238 KB

english, 1998

35

Molecular Dynamics Simulations of NAD+-Induced Domain Closure in Horse Liver Alcohol Dehydrogenase

Hayward, Steven, Kitao, Akio

Journal:

Biophysical Journal

Year:

2006

Language:

english

File:

PDF, 711 KB

english, 2006

36

Hydration Effect on Low-Frequency Protein Dynamics Observed in Simulated Neutron Scattering Spectra

Joti, Yasumasa, Nakagawa, Hiroshi, Kataoka, Mikio, Kitao, Akio

Journal:

Biophysical Journal

Year:

2008

Language:

english

File:

PDF, 298 KB

english, 2008

37

Thermal Unfolding Simulations of Bacterial Flagellin: Insight into its Refolding Before Assembly

Chng, Choon-Peng, Kitao, Akio

Journal:

Biophysical Journal

Year:

2008

Language:

english

File:

PDF, 866 KB

english, 2008

38

A theoretical study of the two binding modes between lysozyme and tri-NAG with an explicit solvent model based on the fragment molecular orbital method

Ishikawa, Takeshi, Burri, Raghunadha Reddy, Kamatari, Yuji O., Sakuraba, Shun, Matubayasi, Nobuyuki, Kitao, Akio, Kuwata, Kazuo

Journal:

Physical Chemistry Chemical Physics

Year:

2013

Language:

english

File:

PDF, 2.49 MB

english, 2013

39

Exploring the Folding Free Energy Landscape of a β-Hairpin Miniprotein, Chignolin, Using Multiscale Free Energy Landscape Calculation Method

Harada, Ryuhei, Kitao, Akio

Journal:

Journal of Physical Chemistry B

Year:

2011

Language:

english

File:

PDF, 2.66 MB

english, 2011

40

Free-energy analysis of lysozyme–triNAG binding modes with all-atom molecular dynamics simulation combined with the solution theory in the energy representation

Takemura, Kazuhiro, Burri, Raghunadha Reddy, Ishikawa, Takeshi, Ishikura, Takakazu, Sakuraba, Shun, Matubayasi, Nobuyuki, Kuwata, Kazuo, Kitao, Akio

Journal:

Chemical Physics Letters

Year:

2013

Language:

english

File:

PDF, 540 KB

english, 2013

41

CyClus: A fast, comprehensive cylindrical interface approximation clustering/reranking method for rigid-body protein-protein docking decoys

Omori, Satoshi, Kitao, Akio

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

2013

Language:

english

File:

PDF, 729 KB

english, 2013

42

The Fast-Folding Mechanism of Villin Headpiece Subdomain Studied by Multiscale Distributed Computing

Harada, Ryuhei, Kitao, Akio

Journal:

Journal of Chemical Theory and Computation

Year:

2012

Language:

english

File:

PDF, 3.24 MB

english, 2012

43

Effects of solvent on the conformation and the collective motions of a protein. 3. Free energy analysis by the extended RISM theory

Kitao, Akio, Hirata, Fumio, Go, Nobuhiro

Journal:

Journal of Physical Chemistry

Year:

1993

Language:

english

File:

PDF, 638 KB

english, 1993

44

Free Energy Landscape of Biomolecules from Multiple Non-Equilibrium Molecular Simulations

Sakuraba, Shun, Kitao, Akio

Journal:

Biophysical Journal

Year:

2009

Language:

english

File:

PDF, 80 KB

english, 2009

45

A Molecular Simulation Study to Investigate Actin Filament Elongation Mechanism

Wakai, Nobuhiko, Nishihara, Yasutaka, Takemura, Kazuhiro, Fujii, Takashi, Namba, Keiichi, Kitao, Akio

Journal:

Biophysical Journal

Year:

2014

Language:

english

File:

PDF, 47 KB

english, 2014

46

Free Energy Calculation of Protein Conformational Changes using Parallel Cascade Selection Molecular Dynamics Simulation and Markov State Model

Nishihara, Yasutaka, Harada, Ryuhei, Kitao, Akio

Journal:

Biophysical Journal

Year:

2014

Language:

english

File:

PDF, 38 KB

english, 2014

47

Multi-Scale Sampling using Temperature Accelerated and Replica Exchange Molecular Dynamics

yu, yamamori, Kitao, Akio

Journal:

Biophysical Journal

Year:

2014

Language:

english

File:

PDF, 124 KB

english, 2014

48

Hydration-Dependent Protein Dynamics Revealed by Molecular Dynamics Simulation of Crystalline Staphylococcal Nuclease

Joti, Yasumasa, Nakagawa, Hiroshi, Kataoka, Mikio, Kitao, Akio

Journal:

Journal of Physical Chemistry B

Year:

2008

Language:

english

File:

PDF, 300 KB

english, 2008

49

Protein Electron Transfer Reorganization Energy Spectrum from Normal Mode Analysis. 2. Application to Ru-Modified Cytochrome c

Basu, Gautam, Kitao, Akio, Kuki, Atsuo, Go, Nobuhiro

Journal:

Journal of Physical Chemistry B

Year:

1998

Language:

english

File:

PDF, 198 KB

english, 1998

50

Protein Boson Peak Originated from Hydration-Related Multiple Minima Energy Landscape

Joti, Yasumasa, Kitao, Akio, Go, Nobuhiro

Journal:

Journal of the American Chemical Society

Year:

2005

Language:

english

File:

PDF, 206 KB

english, 2005

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