IKEGUCHI, Mitsunori: search on Z-Library

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1

Development of interactive biomolecular graphics system LIVE

Takahiro Ishii, Mitsunori Ikeguchi, Toshihiro Yamada, Junta Doi

Journal:

Journal of Molecular Graphics

Year:

1992

Language:

english

File:

PDF, 300 KB

english, 1992

2

Structural Characterization of the Histone Multimers in the Gas Phase using Ion Mobility Mass Spectrometry and Molecular Dynamics Simulation

Saikusa, Kazumi, Fuchigami, Sotaro, Takahashi, Kyohei, Asano, Yuuki, Nagadoi, Aritaka, Tachiwana, Hiroaki, Kurumizaka, Hitoshi, Ikeguchi, Mitsunori, Nishimura, Yoshifumi, Akashi, Satoko

Journal:

Biophysical Journal

Year:

2014

Language:

english

File:

PDF, 43 KB

english, 2014

3

Dissection of the angle of single fluorophore attached to the nucleotide in corkscrewing microtubules

Fujimura, Shoko, Ito, Yuko, Ikeguchi, Mitsunori, Adachi, Kengo, Yajima, Junichiro, Nishizaka, Takayuki

Journal:

Biochemical and Biophysical Research Communications

Year:

2017

Language:

english

File:

PDF, 1.44 MB

english, 2017

4

3P165 Rotation mechanism of V_1-ATPase studied by steered MD simulations(11. Molecular motor,Poster)

Isaka, Yuta, Yamato, Ichiro, Murata, Takeshi, Ikeguchi, Mitsunori

Journal:

Seibutsu Butsuri

Year:

2013

Language:

english

File:

PDF, 693 KB

english, 2013

5

Finite-Size Effect on the Charging Free Energy in the Alchemical Perturbation and “Warp Drive” Method

Ekimoto, Toru, Yamane, Tsutomu, Ikeguchi, Mitsunori

Journal:

Biophysical Journal

Year:

2018

Language:

english

File:

PDF, 37 KB

english, 2018

6

Elimination of Finite-Size Effects on Binding Free Energies via the Warp-Drive Method

Ekimoto, Toru, Yamane, Tsutomu, Ikeguchi, Mitsunori

Journal:

Journal of Chemical Theory and Computation

Year:

2018

Language:

english

File:

PDF, 3.98 MB

english, 2018

7

Parallel algorithm for efficient calculation of second derivatives of conformational energy function in internal coordinates

Nakamura, Shugo, Ikeguchi, Mitsunori, Shimizu, Kentaro

Journal:

Journal of Computational Chemistry

Year:

1998

Language:

english

File:

PDF, 219 KB

english, 1998

8

Prediction of protein structure classes and secondary structures by means of hidden Markov models

Hiroshi Yoshikawa, Mitsunori Ikeguchi, Shugo Nakamura, Kentaro Shimizu, Junta Doi

Journal:

Systems and Computers in Japan

Year:

1999

Language:

english

File:

PDF, 267 KB

english, 1999

9

New method for parallel computation of Hessian matrix of conformational energy function in internal coordinates

Shugo Nakamura, Daisuke Kyono, Mitsunori Ikeguchi, Kentaro Shimizu

Journal:

Journal of Computational Chemistry

Year:

2002

Language:

english

File:

PDF, 195 KB

english, 2002

10

Partial rigid-body dynamics in NPT, NPAT and NPγT ensembles for proteins and membranes

Mitsunori Ikeguchi

Journal:

Journal of Computational Chemistry

Year:

2004

Language:

english

File:

PDF, 279 KB

english, 2004

11

Linear response theory in dihedral angle space for protein structural change upon ligand binding

Satoshi Omori, Sotaro Fuchigami, Mitsunori Ikeguchi, Akinori Kidera

Journal:

Journal of Computational Chemistry

Year:

2009

Language:

english

File:

PDF, 429 KB

english, 2009

12

Structural fluctuation and concerted motions in F1-ATPase: A molecular dynamics study

Yuko Ito, Mitsunori Ikeguchi

Journal:

Journal of Computational Chemistry

Year:

2010

Language:

english

File:

PDF, 9.96 MB

english, 2010

13

Protein folding simulation using empirical potentials from homological analysis

Toshihiro Yamada, Mitsunori Ikeguchi, Junta Doi

Journal:

Journal of Molecular Graphics

Year:

1990

Language:

english

File:

PDF, 135 KB

english, 1990

14

Physical basis for characterizing native structures of proteins

Yuichi Harano, Roland Roth, Yuji Sugita, Mitsunori Ikeguchi, Masahiro Kinoshita

Journal:

Chemical Physics Letters

Year:

2007

Language:

english

File:

PDF, 219 KB

english, 2007

15

Molecular dynamics simulations of the isolated β subunit of F1-ATPase

Yuko Ito, Mitsunori Ikeguchi

Journal:

Chemical Physics Letters

Year:

2010

Language:

english

File:

PDF, 626 KB

english, 2010

16

Dynamical analysis of tRNAGln–GlnRS complex using normal mode calculation

Shugo Nakamura, Mitsunori Ikeguchi, Kentaro Shimizu

Journal:

Chemical Physics Letters

Year:

2003

Language:

english

File:

PDF, 675 KB

english, 2003

17

Extracting contact free energy from solubility: excluded volume effects of polymers in continuum space

Seishi Shimizu, Mitsunori Ikeguchi, Kentaro Shimizu

Journal:

Chemical Physics Letters

Year:

1997

Language:

english

File:

PDF, 590 KB

english, 1997

18

An off-lattice theory of solvation: extension of the Flory χ parameter into continuum space

Seishi Shimizu, Mitsunori Ikeguchi, Kentaro Shimizu

Journal:

Chemical Physics Letters

Year:

1998

Language:

english

File:

PDF, 127 KB

english, 1998

19

Molecular volume, surface area, and curvature dependence of the configurational entropy change upon solvation: effects of molecular bonding

Seishi Shimizu, Mitsunori Ikeguchi, Shugo Nakamura, Kentaro Shimizu

Journal:

Chemical Physics Letters

Year:

1998

Language:

english

File:

PDF, 122 KB

english, 1998

20

Calculation of temperature dependence of free energy caused by potential function changes

Mitsunori Ikeguchi, Seishi Shimizu, Koichi Tazaki, Shugo Nakamura, Kentaro Shimizu

Journal:

Chemical Physics Letters

Year:

1998

Language:

english

File:

PDF, 108 KB

english, 1998

21

Structural modeling of DNA mini-hairpin molecules with various loop sequences

Shugo Nakamura, Hitoshi Hirose, Mitsunori Ikeguchi, Kentaro Shimizu

Journal:

Chemical Physics Letters

Year:

1999

Language:

english

File:

PDF, 179 KB

english, 1999

22

Water-mediated interactions between DNA and PhoB DNA-binding/transactivation domain: NMR-restrained molecular dynamics in explicit water environment

Tsutomu Yamane, Hideyasu Okamura, Mitsunori Ikeguchi, Yoshifumi Nishimura, Akinori Kidera

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

2008

Language:

english

File:

PDF, 1.24 MB

english, 2008

23

Free-energy function based on an all-atom model for proteins

Takashi Yoshidome, Koji Oda, Yuichi Harano, Roland Roth, Yuji Sugita, Mitsunori Ikeguchi, Masahiro Kinoshita

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

2009

Language:

english

File:

PDF, 543 KB

english, 2009

24

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

25

The crystal structure of the tryptophan synthase β2 subunit from the hyperthermophile Pyrococcus furiosus : Investigation of stabilization factors

Yusaku Hioki, Kyoko Ogasahara, Soo Jae Lee, Jichun Ma, Masami Ishida, Yuriko Yamagata, Yoshiki Matsuura, Motonori Ota, Mitsunori Ikeguchi, Seiki Kuramitsu, Katsuhide Yutani

Journal:

Year:

2004

Language:

english

File:

PDF, 603 KB

english, 2004

26

Homology-modelled structure of the βB2B3-crystallin heterodimer studied by ion mobility and radical probe MS

Kevin M. Downard, Yuichi Kokabu, Mitsunori Ikeguchi, Satoko Akashi

Journal:

Year:

2011

Language:

english

File:

PDF, 687 KB

english, 2011

27

Fission yeast Swi5/Sfr1 and Rhp55/Rhp57 differentially regulate Rhp51-dependent recombination outcomes

Akamatsu, Yufuko, Tsutsui, Yasuhiro, Morishita, Takashi, Siddique, MD Shahjahan P, Kurokawa, Yumiko, Ikeguchi, Mitsunori, Yamao, Fumiaki, Arcangioli, Benoit, Iwasaki, Hiroshi

Journal:

The EMBO Journal

Year:

2007

Language:

english

File:

PDF, 389 KB

english, 2007

28

Molecular Mechanism of ATP Hydrolysis in F 1 -ATPase Revealed by Molecular Simulations and Single-Molecule Observations

Hayashi, Shigehiko, Ueno, Hiroshi, Shaikh, Abdul Rajjak, Umemura, Myco, Kamiya, Motoshi, Ito, Yuko, Ikeguchi, Mitsunori, Komoriya, Yoshihito, Iino, Ryota, Noji, Hiroyuki

Journal:

Journal of the American Chemical Society

Year:

2012

Language:

english

File:

PDF, 3.20 MB

english, 2012

29

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

30

Mechanistic Insights into the Activation of Rad51-Mediated Strand Exchange from the Structure of a Recombination Activator, the Swi5-Sfr1 Complex

Naoyuki Kuwabara, Yasuto Murayama, Hiroshi Hashimoto, Yuuichi Kokabu, Mitsunori Ikeguchi, Mamoru Sato, Kouta Mayanagi, Yasuhiro Tsutsui, Hiroshi Iwasaki, Toshiyuki Shimizu

Journal:

Year:

2012

Language:

english

File:

PDF, 1.09 MB

english, 2012

31

MD–SAXS method with nonspherical boundaries

Tomotaka Oroguchi, Mitsunori Ikeguchi

Journal:

Chemical Physics Letters

Year:

2012

Language:

english

File:

PDF, 806 KB

english, 2012

32

Comparative simulations of aquaporin family: AQP1, AQPZ, AQP0 and GlpF

Masanori Hashido, Mitsunori Ikeguchi, Akinori Kidera

Journal:

Year:

2005

Language:

english

File:

PDF, 322 KB

english, 2005

33

Atomically Detailed Description of the Unfolding of α-Lactalbumin by the Combined Use of Experiments and Simulations

Tomotaka Oroguchi, Mitsunori Ikeguchi, Kimiko Saeki, Kiyoto Kamagata, Yoriko Sawano, Masaru Tanokura, Akinori Kidera, Kunihiro Kuwajima

Journal:

Journal of Molecular Biology

Year:

2005

Language:

english

File:

PDF, 550 KB

english, 2005

34

Unfolding Pathways of Goat α-Lactalbumin as Revealed in Multiple Alignment of Molecular Dynamics Trajectories

Tomotaka Oroguchi, Mitsunori Ikeguchi, Motonori Ota, Kunihiro Kuwajima, Akinori Kidera

Journal:

Journal of Molecular Biology

Year:

2007

Language:

english

File:

PDF, 1.08 MB

english, 2007

35

Classification and Annotation of the Relationship between Protein Structural Change and Ligand Binding

Takayuki Amemiya, Ryotaro Koike, Sotaro Fuchigami, Mitsunori Ikeguchi, Akinori Kidera

Journal:

Journal of Molecular Biology

Year:

2011

Language:

english

File:

PDF, 2.18 MB

english, 2011

36

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

37

Intrinsic Dynamics of Restriction Endonuclease EcoO109I Studied by Molecular Dynamics Simulations and X-Ray Scattering Data Analysis

Oroguchi, Tomotaka, Hashimoto, Hiroshi, Shimizu, Toshiyuki, Sato, Mamoru, Ikeguchi, Mitsunori

Journal:

Biophysical Journal

Year:

2009

Language:

english

File:

PDF, 3.14 MB

english, 2009

38

Structure Analysis of F1-ATPase via Molecular Dynamics

Ito, Yuko, Ikeguchi, Mitsunori

Journal:

Biophysical Journal

Year:

2009

Language:

english

File:

PDF, 39 KB

english, 2009

39

Role of the DELSEED Loop in Torque Transmission of F1-ATPase

Tanigawara, Mizue, Tabata, Kazuhito V., Ito, Yuko, Ito, Jotaro, Watanabe, Rikiya, Ueno, Hiroshi, Ikeguchi, Mitsunori, Noji, Hiroyuki

Journal:

Biophysical Journal

Year:

2012

Language:

english

File:

PDF, 892 KB

english, 2012

40

Water Transport in Aquaporins: Osmotic Permeability Matrix Analysis of Molecular Dynamics Simulations

Hashido, Masanori, Kidera, Akinori, Ikeguchi, Mitsunori

Journal:

Biophysical Journal

Year:

2007

Language:

english

File:

PDF, 1.13 MB

english, 2007

41

Effects of ionic strength on SAXS data for proteins revealed by molecular dynamics simulations

Oroguchi, Tomotaka, Ikeguchi, Mitsunori

Journal:

The Journal of Chemical Physics

Year:

2011

Language:

english

File:

PDF, 990 KB

english, 2011

42

Protein Structural Change Upon Ligand Binding: Linear Response Theory

Ikeguchi, Mitsunori, Ueno, Jiro, Sato, Miwa, Kidera, Akinori

Journal:

Physical Review Letters

Year:

2005

Language:

english

File:

PDF, 968 KB

english, 2005

43

A Native Disulfide Stabilizes Non-Native Helical Structures in Partially Folded States of Equine β-Lactoglobulin

Yamamoto, Mio, Nakagawa, Kanako, Fujiwara, Kazuo, Shimizu, Akio, Ikeguchi, Mitsunori, Ikeguchi, Masamichi

Journal:

Year:

2011

Language:

english

File:

PDF, 533 KB

english, 2011

44

Molecular Modeling and Molecular Dynamics Simulations of Recombinase Rad51

Kokabu, Yuichi, Ikeguchi, Mitsunori

Journal:

Biophysical Journal

Year:

2013

Language:

english

File:

PDF, 35 KB

english, 2013

45

Mechanism of the Conformational Change of the F 1 -ATPase β Subunit Revealed by Free Energy Simulations

Ito, Yuko, Oroguchi, Tomotaka, Ikeguchi, Mitsunori

Journal:

Journal of the American Chemical Society

Year:

2011

Language:

english

File:

PDF, 5.84 MB

english, 2011

46

Functional Rotation Induced by Alternating Protonation States in the Multidrug Transporter AcrB: All-Atom Molecular Dynamics Simulations

Yamane, Tsutomu, Murakami, Satoshi, Ikeguchi, Mitsunori

Journal:

Year:

2013

Language:

english

File:

PDF, 1.64 MB

english, 2013

47

Analysis Of Side-chain Dynamics Of PhoB Dna Binding/transactivation Domain Using Molecular Dynamics Simulations

Yamane, Tsutomu, Okamura, Hideyasu, Nishimura, Yoshifumi, Kidera, Akinori, Ikeguchi, Mitsunori

Journal:

Biophysical Journal

Year:

2009

Language:

english

File:

PDF, 36 KB

english, 2009

48

Molecular Dynamics Simulations of Yeast F1-ATPase Before and after 16-Degree Rotation of the Gamma Subunit

Ito, Yuko, Yoshidome, Takashi, Matubayasi, Nobuyuki, Kinoshita, Masahiro, Ikeguchi, Mitsunori

Journal:

Biophysical Journal

Year:

2013

Language:

english

File:

PDF, 38 KB

english, 2013

49

All-Atom Molecular Dynamics Simulation of Bacterial Multidrug Efflux Transporters AcrB

Yamane, Tsutomu, Ikeguchi, Mitsunori

Journal:

Biophysical Journal

Year:

2010

Language:

english

File:

PDF, 39 KB

english, 2010

50

All-Atom Molecular Dynamics Simulation of Multidrug Efflux Transporter AcrB

Yamane, Tsutomu, Ikeguchi, Mitsunori

Journal:

Biophysical Journal

Year:

2012

Language:

english

File:

PDF, 37 KB

english, 2012